1
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Lu L, Gou X, Tan SK, Mann SI, Yang H, Zhong X, Gazgalis D, Valdiviezo J, Jo H, Wu Y, Diolaiti ME, Ashworth A, Polizzi NF, DeGrado WF. De novo design of drug-binding proteins with predictable binding energy and specificity. Science 2024; 384:106-112. [PMID: 38574125 DOI: 10.1126/science.adl5364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
The de novo design of small molecule-binding proteins has seen exciting recent progress; however, high-affinity binding and tunable specificity typically require laborious screening and optimization after computational design. We developed a computational procedure to design a protein that recognizes a common pharmacophore in a series of poly(ADP-ribose) polymerase-1 inhibitors. One of three designed proteins bound different inhibitors with affinities ranging from <5 nM to low micromolar. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free energy calculations performed directly on the designed models were in excellent agreement with the experimentally measured affinities. We conclude that de novo design of high-affinity small molecule-binding proteins with tuned interaction energies is feasible entirely from computation.
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Affiliation(s)
- Lei Lu
- Department of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Xuxu Gou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Samuel I Mann
- Department of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Xiaofang Zhong
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Dimitrios Gazgalis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Jesús Valdiviezo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Morgan E Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Nicholas F Polizzi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry & Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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2
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Van Loon K, Breithaupt L, Ng D, DeBoer RJ, Buckle GC, Bialous S, Hiatt RA, Volberding P, Hermiston ML, Ashworth A. A roadmap to establishing global oncology as a priority initiative within a National Cancer Institute-designated cancer center. J Natl Cancer Inst 2024; 116:345-351. [PMID: 38060289 PMCID: PMC10919326 DOI: 10.1093/jnci/djad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
As the burden of cancers impacting low- and middle-income countries is projected to increase, formation of strategic partnerships between institutions in high-income countries and low- and middle-income country institutions may serve to accelerate cancer research, clinical care, and training. As the US National Cancer Institute and its Center for Global Health continue to encourage cancer centers to join its global mission, academic cancer centers in the United States have increased their global activities. In 2015, the Helen Diller Family Comprehensive Cancer Center at the University of California, San Francisco, responded to the call for international partnership in addressing the global cancer burden through the establishment of the Global Cancer Program as a priority initiative. In developing the Global Cancer Program, we galvanized institutional support to foster sustained, bidirectional, equitable, international partnerships in global cancer control. Our focus and intent in disseminating this commentary is to share experiences and lessons learned from the perspective of a US-based, National Cancer Institute-designated cancer center and to provide a roadmap for other high-income institutions seeking to strategically broaden their missions and address the complex challenges of global cancer control. Herein, we review the formative evaluation, governance, strategic planning, investments in career development, funding sources, program evaluation, and lessons learned. Reflecting on the evolution of our program during the first 5 years, we observed in our partners a powerful shift toward a locally driven priority setting, reduced dependency, and an increased commitment to research as a path to improve cancer outcomes in resource-constrained settings.
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Affiliation(s)
- Katherine Van Loon
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Medicine, Division of Hematology/Oncology, UCSF, San Francisco, CA, USA
| | - Lindsay Breithaupt
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Dianna Ng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Pathology, UCSF, San Francisco, CA, USA
| | - Rebecca J DeBoer
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Medicine, Division of Hematology/Oncology, UCSF, San Francisco, CA, USA
| | - Geoffrey C Buckle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Medicine, Division of Hematology/Oncology, UCSF, San Francisco, CA, USA
| | - Stella Bialous
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- School of Nursing, UCSF, San Francisco, CA, USA
| | - Robert A Hiatt
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - Paul Volberding
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
| | - Michelle L Hermiston
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, UCSF, San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Medicine, Division of Hematology/Oncology, UCSF, San Francisco, CA, USA
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3
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Yang Y, Badura ML, O’Leary PC, Delavan HM, Robinson TM, Egusa EA, Zhong X, Swinderman JT, Li H, Zhang M, Kim M, Ashworth A, Feng FY, Chou J, Yang L. Large tandem duplications in cancer result from transcription and DNA replication collisions. medRxiv 2024:2023.05.17.23290140. [PMID: 38260434 PMCID: PMC10802642 DOI: 10.1101/2023.05.17.23290140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Despite the abundance of somatic structural variations (SVs) in cancer, the underlying molecular mechanisms of their formation remain unclear. Here, we use 6,193 whole-genome sequenced tumors to study the contributions of transcription and DNA replication collisions to genome instability. After deconvoluting robust SV signatures in three independent pan-cancer cohorts, we detect transcription-dependent replicated-strand bias, the expected footprint of transcription-replication collision (TRC), in large tandem duplications (TDs). Large TDs are abundant in female-enriched, upper gastrointestinal tract and prostate cancers. They are associated with poor patient survival and mutations in TP53, CDK12, and SPOP. Upon inactivating CDK12, cells display significantly more TRCs, R-loops, and large TDs. Inhibition of G2/M checkpoint proteins, such as WEE1, CHK1, and ATR, selectively inhibits the growth of cells deficient in CDK12. Our data suggest that large TDs in cancer form due to TRCs, and their presence can be used as a biomarker for prognosis and treatment.
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Affiliation(s)
- Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Michelle L. Badura
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Patrick C. O’Leary
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Henry M. Delavan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Troy M. Robinson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Emily A. Egusa
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Jason T. Swinderman
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
| | - Minkyu Kim
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Department of Cellular Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- University of Chicago Comprehensive Cancer Center, Chicago, IL, USA
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4
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Lu L, Gou X, Tan SK, Mann SI, Yang H, Zhong X, Gazgalis D, Valdiviezo J, Jo H, Wu Y, Diolaiti ME, Ashworth A, Polizzi NF, DeGrado WF. De novo design of drug-binding proteins with predictable binding energy and specificity. bioRxiv 2023:2023.12.23.573178. [PMID: 38187746 PMCID: PMC10769398 DOI: 10.1101/2023.12.23.573178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low μM, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles.
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Affiliation(s)
- Lei Lu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xuxu Gou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Samuel I. Mann
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Dimitrios Gazgalis
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jesús Valdiviezo
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Morgan E. Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | | | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
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5
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Bank EM, Small EJ, Ashworth A, Hiatt RA. Cancer Research in 2030: A unique strategic planning process at a comprehensive cancer center. Prev Oncol Epidemiol 2023; 1:1-9. [PMID: 38525348 PMCID: PMC10959521 DOI: 10.1080/28322134.2023.2265563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/27/2023] [Indexed: 03/26/2024]
Abstract
Following the successful renewal of its Cancer Center Support Grant (CCSG), leadership of the UCSF Helen Diller Comprehensive Cancer Center (HDFCCC) began a strategic planning process. The motivation was to think about where cancer research was going in the future; and with this vision to define a general scientific direction, mission, and priorities. HDFCCC Leadership began discussions about a new strategic plan in early 2018. From these meetings, the theme of "Cancer Research in 2030" arose: that is, what will cancer research look like in 2030? This forward-looking focus was intended to encourage creativity unconfined by a particular institutional structure or grant mechanism. Focusing on the science paved the way for an innovative, actionable, and motivating strategic planning process. Here, we describe the three-phase process, and the various groups involved across the HDFCCC and UCSF. We present the unique framework based on a cells-to-society model and an individual experience perspective, which led to the development of a logic model and ongoing implementation of tactics and tracking progress. We believe that sharing this process and its results will be of value to cancer centers and cancer researchers across the network of NCI comprehensive cancer centers, and cancer research centers in general.
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Affiliation(s)
- Erin M. Bank
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
| | - Eric J. Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
| | - Robert A. Hiatt
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
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6
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Taha TY, Suryawanshi RK, Chen IP, Correy GJ, McCavitt-Malvido M, O’Leary PC, Jogalekar MP, Diolaiti ME, Kimmerly GR, Tsou CL, Gascon R, Montano M, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo. PLoS Pathog 2023; 19:e1011614. [PMID: 37651466 PMCID: PMC10499221 DOI: 10.1371/journal.ppat.1011614] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/13/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the role of Mac1 catalytic activity in viral replication, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by ~10-fold, mutations to aspartic acid (N40D) reduced activity by ~100-fold relative to wild-type. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, the N40D mutant replicated at >1000-fold lower levels compared to the wild-type virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection. Our data validate the critical role of SARS-CoV-2 NSP3 Mac1 catalytic activity in viral replication and as a promising therapeutic target to develop antivirals.
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Affiliation(s)
- Taha Y. Taha
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Rahul K. Suryawanshi
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Irene P. Chen
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Galen J. Correy
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Maria McCavitt-Malvido
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Patrick C. O’Leary
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Manasi P. Jogalekar
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Morgan E. Diolaiti
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Gabriella R. Kimmerly
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Chia-Lin Tsou
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Ronnie Gascon
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Mauricio Montano
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Luis Martinez-Sobrido
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Alan Ashworth
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - James S. Fraser
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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7
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Choudhury A, Cady MA, Lucas CHG, Najem H, Phillips JJ, Palikuqi B, Zakimi N, Joseph T, Birrueta JO, Chen WC, Bush NAO, Hervey-Jumper SL, Klein OD, Toedebusch CM, Horbinski CM, Magill ST, Bhaduri A, Perry A, Dickinson PJ, Heimberger AB, Ashworth A, Crouch EE, Raleigh DR. NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy. bioRxiv 2023:2023.07.10.548456. [PMID: 37503127 PMCID: PMC10369862 DOI: 10.1101/2023.07.10.548456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Meningiomas are the most common primary intracranial tumors1-3. Treatments for patients with meningiomas are limited to surgery and radiotherapy, and systemic therapies remain ineffective or experimental4,5. Resistance to radiotherapy is common in high-grade meningiomas6, and the cell types and signaling mechanisms driving meningioma tumorigenesis or resistance to radiotherapy are incompletely understood. Here we report NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy and find NOTCH3+ meningioma mural cells are conserved across meningiomas from humans, dogs, and mice. NOTCH3+ cells are restricted to the perivascular niche during meningeal development and homeostasis and in low-grade meningiomas but are expressed throughout high-grade meningiomas that are resistant to radiotherapy. Integrating single-cell transcriptomics with lineage tracing and imaging approaches across mouse genetic and xenograft models, we show NOTCH3 drives tumor initiating capacity, cell proliferation, angiogenesis, and resistance to radiotherapy to increase meningioma growth and reduce survival. An antibody stabilizing the extracellular negative regulatory region of NOTCH37,8 blocks meningioma tumorigenesis and sensitizes meningiomas to radiotherapy, reducing tumor growth and improving survival in preclinical models. In summary, our results identify a conserved cell type and signaling mechanism that underlie meningioma tumorigenesis and resistance to radiotherapy, revealing a new therapeutic vulnerability to treat meningiomas that are resistant to standard interventions.
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Affiliation(s)
- Abrar Choudhury
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Martha A. Cady
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Calixto-Hope G. Lucas
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
| | - Hinda Najem
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Brisa Palikuqi
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Naomi Zakimi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Tara Joseph
- Department of Pediatrics, University of California San Francisco, San Francisco, CA,USA
| | - Janeth Ochoa Birrueta
- Department of Pediatrics, University of California San Francisco, San Francisco, CA,USA
| | - William C. Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Shawn L. Hervey-Jumper
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ophir D. Klein
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Christine M. Toedebusch
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Craig M. Horbinski
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | - Stephen T. Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Peter J. Dickinson
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Amy B. Heimberger
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Alan Ashworth
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Elizabeth E. Crouch
- Department of Pediatrics, University of California San Francisco, San Francisco, CA,USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - David R. Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
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8
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Taha TY, Suryawanshi RK, Chen IP, Correy GJ, O'Leary PC, Jogalekar MP, McCavitt-Malvido M, Diolaiti ME, Kimmerly GR, Tsou CL, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo. bioRxiv 2023:2023.04.18.537104. [PMID: 37131711 PMCID: PMC10153184 DOI: 10.1101/2023.04.18.537104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the therapeutic potential of Mac1 inhibition, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by ~10-fold, mutations to aspartic acid (N40D) reduced activity by ~100-fold relative to wildtype. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, N40D replicated at >1000-fold lower levels compared to the wildtype virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection and showed no signs of lung pathology. Our data validate the SARS-CoV-2 NSP3 Mac1 domain as a critical viral pathogenesis factor and a promising target to develop antivirals.
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Affiliation(s)
- Taha Y Taha
- Gladstone Institutes, San Francisco, CA 94158
| | | | - Irene P Chen
- Gladstone Institutes, San Francisco, CA 94158
- University of California San Francisco, San Francisco, CA 94158
| | - Galen J Correy
- University of California San Francisco, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | | | | | | | | | | | | | | | - Nevan J Krogan
- University of California San Francisco, San Francisco, CA 94158
| | - Alan Ashworth
- University of California San Francisco, San Francisco, CA 94158
| | - James S Fraser
- University of California San Francisco, San Francisco, CA 94158
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158
- University of California San Francisco, San Francisco, CA 94158
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158
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9
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Mandair D, Reis-Filho JS, Ashworth A. Biological insights and novel biomarker discovery through deep learning approaches in breast cancer histopathology. NPJ Breast Cancer 2023; 9:21. [PMID: 37024522 PMCID: PMC10079681 DOI: 10.1038/s41523-023-00518-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/27/2023] [Indexed: 04/08/2023] Open
Abstract
Breast cancer remains a highly prevalent disease with considerable inter- and intra-tumoral heterogeneity complicating prognostication and treatment decisions. The utilization and depth of genomic, transcriptomic and proteomic data for cancer has exploded over recent times and the addition of spatial context to this information, by understanding the correlating morphologic and spatial patterns of cells in tissue samples, has created an exciting frontier of research, histo-genomics. At the same time, deep learning (DL), a class of machine learning algorithms employing artificial neural networks, has rapidly progressed in the last decade with a confluence of technical developments - including the advent of modern graphic processing units (GPU), allowing efficient implementation of increasingly complex architectures at scale; advances in the theoretical and practical design of network architectures; and access to larger datasets for training - all leading to sweeping advances in image classification and object detection. In this review, we examine recent developments in the application of DL in breast cancer histology with particular emphasis of those producing biologic insights or novel biomarkers, spanning the extraction of genomic information to the use of stroma to predict cancer recurrence, with the aim of suggesting avenues for further advancing this exciting field.
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Affiliation(s)
- Divneet Mandair
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
| | | | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA.
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10
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Yang Y, Badura M, O’Leary P, Egusa E, Robinson T, Zhong X, Swinderman J, Kim M, Li H, Ashworth A, Feng F, Chou J, Yang L. Abstract 299: Large tandem duplications in cancer resulting from transcription and DNA replication collisions. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Somatic structural variations (SVs) are common in cancer. Although a small fraction of SVs in breast and ovarian cancers can be attributed to homologous recombination deficiency, the underlying molecular mechanisms for the vast majority of somatic SVs remain unclear. Here, we focus on the roles of transcription and DNA replication collisions in genomic instability in cancer. Such collisions are unavoidable in cells since both transcription and replication use the same DNA as template. We hypothesized that transcription replication collisions (TRCs), if not properly repaired, would lead to collapsed replication forks and result in SVs. To this end, we studied somatic SVs in 5994 high-coverage whole-genome sequenced primary and metastatic tumors from three independent pan-cancer cohorts. A total of 12 conserved SV signatures, representing independent molecular mechanisms, were deconvoluted from these cohorts using non-negative matrix factorization approach. We detected replicated-strand bias, the expected footprint of transcription-replication collision, in large tandem duplications (TDs) across multiple cohorts. This bias was only observed in expressed genes, consistent with TRCs depending on transcription activity. Large TDs were abundant in female-specific (breast, ovarian and uterus), upper gastric-intestinal tract and prostate cancers. They were associated with worse patient survival and TP53 and CDK12 mutations. CDK12 is a cyclin-dependent kinase (CDK) and a key regulator of transcription elongation. Deleting or suppressing CDK12 using CRISPR-Cas9 in prostate cancer cell lines not only increased RNA:DNA hybrids (R-loops), but also promoted TRCs, suggesting a mechanism by which dysregulation of a transcriptional CDK may lead to genomic instability. Finally, using existing large-scale drug screening data, we found that cancer cell lines with abundant large TDs were significantly more sensitive to the WEE1 inhibitor, MK-1775, which we experimentally validated in prostate cancer cells lacking CDK12. In summary, our data suggest that large TDs in cancer form due to impaired TRC repair and can be used as a biomarker for prognosis and treatment.
Citation Format: Yang Yang, Michelle Badura, Patrick O’Leary, Emily Egusa, Troy Robinson, Xiaoming Zhong, Jason Swinderman, Minkyu Kim, Haolong Li, Alan Ashworth, Felix Feng, Jonathan Chou, Lixing Yang. Large tandem duplications in cancer resulting from transcription and DNA replication collisions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 299.
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Affiliation(s)
| | | | | | - Emily Egusa
- 2University of California, San Francisco, San Francisco, CA
| | - Troy Robinson
- 2University of California, San Francisco, San Francisco, CA
| | | | | | - Minkyu Kim
- 2University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- 2University of California, San Francisco, San Francisco, CA
| | - Alan Ashworth
- 2University of California, San Francisco, San Francisco, CA
| | - Felix Feng
- 2University of California, San Francisco, San Francisco, CA
| | - Jonathan Chou
- 2University of California, San Francisco, San Francisco, CA
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11
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Calses PC, Pham VC, Guarnaccia AD, Choi M, Verschueren E, Bakker ST, Pham TH, Hinkle T, Liu C, Chang MT, Kljavin N, Bakalarski C, Haley B, Zou J, Yan C, Song X, Lin X, Rowntree R, Ashworth A, Dey A, Lill JR. TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage. Mol Cell Proteomics 2023; 22:100496. [PMID: 36640924 PMCID: PMC9947421 DOI: 10.1016/j.mcpro.2023.100496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Transcriptional enhanced associate domain family members 1 to 4 (TEADs) are a family of four transcription factors and the major transcriptional effectors of the Hippo pathway. In order to activate transcription, TEADs rely on interactions with other proteins, such as the transcriptional effectors Yes-associated protein and transcriptional co-activator with PDZ-binding motif. Nuclear protein interactions involving TEADs influence the transcriptional regulation of genes involved in cell growth, tissue homeostasis, and tumorigenesis. Clearly, protein interactions for TEADs are functionally important, but the full repertoire of TEAD interaction partners remains unknown. Here, we employed an affinity purification mass spectrometry approach to identify nuclear interacting partners of TEADs. We performed affinity purification mass spectrometry experiment in parallel in two different cell types and compared a wildtype TEAD bait protein to a nuclear localization sequence mutant that does not localize to the nucleus. We quantified the results using SAINT analysis and found a significant enrichment of proteins linked to DNA damage including X-ray repair cross-complementing protein 5 (XRCC5), X-ray repair cross-complementing protein 6 (XRCC6), poly(ADP-ribose) polymerase 1 (PARP1), and Rap1-interacting factor 1 (RIF1). In cellular assays, we found that TEADs co-localize with DNA damage-induced nuclear foci marked by histone H2AX phosphorylated on S139 (γH2AX) and Rap1-interacting factor 1. We also found that depletion of TEAD proteins makes cells more susceptible to DNA damage by various agents and that depletion of TEADs promotes genomic instability. Additionally, depleting TEADs dampens the efficiency of DNA double-stranded break repair in reporter assays. Our results connect TEADs to DNA damage response processes, positioning DNA damage as an important avenue for further research of TEAD proteins.
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Affiliation(s)
- Philamer C Calses
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA; Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Victoria C Pham
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Alissa D Guarnaccia
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA; Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Meena Choi
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Erik Verschueren
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Sietske T Bakker
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Trang H Pham
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA
| | - Trent Hinkle
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Chad Liu
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA
| | - Matthew T Chang
- Department of Bioinformatics, Genentech Inc, South San Francisco, California, USA
| | - Noelyn Kljavin
- Department of Molecular Oncology, Genentech Inc, South San Francisco, California, USA
| | - Corey Bakalarski
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA
| | - Benjamin Haley
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA
| | - Jianing Zou
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Cuicui Yan
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Xia Song
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Xiaoyan Lin
- Department of Biology, Research Service Division, WuXi AppTec, Shanghai, China
| | - Rebecca Rowntree
- Department of Molecular Oncology, Genentech Inc, South San Francisco, California, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Anwesha Dey
- Departments of Discovery Oncology, Genentech Inc, South San Francisco, California, USA.
| | - Jennie R Lill
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc, South San Francisco, California, USA.
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12
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Chou J, Egusa EA, Wang S, Badura ML, Lee F, Bidkar AP, Zhu J, Shenoy T, Trepka K, Robinson TM, Steri V, Huang J, Wang Y, Small EJ, Chan E, Stohr BA, Ashworth A, Delafontaine B, Rottey S, Cooke KS, Hashemi Sadraei N, Yu B, Salvati M, Bailis JM, Feng FY, Flavell RR, Aggarwal R. Immunotherapeutic Targeting and PET Imaging of DLL3 in Small-Cell Neuroendocrine Prostate Cancer. Cancer Res 2023; 83:301-315. [PMID: 36351060 DOI: 10.1158/0008-5472.can-22-1433] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/06/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022]
Abstract
Effective treatments for de novo and treatment-emergent small-cell/neuroendocrine (t-SCNC) prostate cancer represent an unmet need for this disease. Using metastatic biopsies from patients with advanced cancer, we demonstrate that delta-like ligand 3 (DLL3) is expressed in de novo and t-SCNC and is associated with reduced survival. We develop a PET agent, [89Zr]-DFO-DLL3-scFv, that detects DLL3 levels in mouse SCNC models. In multiple patient-derived xenograft models, AMG 757 (tarlatamab), a half-life-extended bispecific T-cell engager (BiTE) immunotherapy that redirects CD3-positive T cells to kill DLL3-expressing cells, exhibited potent and durable antitumor activity. Late relapsing tumors after AMG 757 treatment exhibited lower DLL3 levels, suggesting antigen loss as a resistance mechanism, particularly in tumors with heterogeneous DLL3 expression. These findings have been translated into an ongoing clinical trial of AMG 757 in de novo and t-SCNC, with a confirmed objective partial response in a patient with histologically confirmed SCNC. Overall, these results identify DLL3 as a therapeutic target in SCNC and demonstrate that DLL3-targeted BiTE immunotherapy has significant antitumor activity in this aggressive prostate cancer subtype. SIGNIFICANCE The preclinical and clinical evaluation of DLL3-directed immunotherapy, AMG 757, and development of a PET radiotracer for noninvasive DLL3 detection demonstrate the potential of targeting DLL3 in SCNC prostate cancer.
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Affiliation(s)
- Jonathan Chou
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Emily A Egusa
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiation Oncology and Urology, University of California, San Francisco, California
| | - Sinan Wang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiology and Biomedical Imaging, University of California, San Francisco, California
| | - Michelle L Badura
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiation Oncology and Urology, University of California, San Francisco, California.,Department of Biology, Santa Clara University, Santa Clara, California
| | - Fei Lee
- Oncology Research, Amgen Research, Amgen, South San Francisco, California
| | - Anil P Bidkar
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California
| | - Jun Zhu
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiation Oncology and Urology, University of California, San Francisco, California
| | - Tanushree Shenoy
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Kai Trepka
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiation Oncology and Urology, University of California, San Francisco, California.,Medical Scientist Training Program, University of California, San Francisco, California
| | - Troy M Robinson
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiation Oncology and Urology, University of California, San Francisco, California
| | - Veronica Steri
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, North Carolina
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia.,Vancouver Prostate Centre, Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric J Small
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Emily Chan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Pathology, University of California, San Francisco, California
| | - Bradley A Stohr
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Pathology, University of California, San Francisco, California
| | - Alan Ashworth
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | | | - Keegan S Cooke
- Oncology Research, Amgen Research, Amgen, Thousand Oaks, California
| | | | - Brian Yu
- Global Development, Amgen, Thousand Oaks, California
| | - Mark Salvati
- Global Development, Amgen, Thousand Oaks, California
| | - Julie M Bailis
- Oncology Research, Amgen Research, Amgen, South San Francisco, California
| | - Felix Y Feng
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiation Oncology and Urology, University of California, San Francisco, California
| | - Robert R Flavell
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Department of Radiology and Biomedical Imaging, University of California, San Francisco, California
| | - Rahul Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
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13
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Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2212931120. [PMID: 36598939 PMCID: PMC9926234 DOI: 10.1073/pnas.2212931120] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.
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Affiliation(s)
- Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Yagmur Umay Doruk
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Moira Rachman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Siyi Wang
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
| | - Dmytro S. Radchenko
- Enamine Ltd., Kyiv02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
| | - Yurii S. Moroz
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
- Chemspace, Kyiv02094, Ukraine
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Adam R. Renslo
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Jenny C. Taylor
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
- Centre for Medicines Discovery, University of Oxford, HeadingtonOX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, HeadingtonOX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park2006, South Africa
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
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14
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Marjon N, Chen J, Diolaiti ME, Renslo A, Ashworth A. 9 Caged rucaparib: cancer directed delivery of PARPi. Gynecol Oncol Rep 2022. [DOI: 10.1016/s2352-5789(22)00221-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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15
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Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J 2022; 289:7399-7410. [PMID: 34323016 PMCID: PMC9027952 DOI: 10.1111/febs.16142] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023]
Abstract
ADP-ribosylation, a modification of proteins, nucleic acids, and metabolites, confers broad functions, including roles in stress responses elicited, for example, by DNA damage and viral infection and is involved in intra- and extracellular signaling, chromatin and transcriptional regulation, protein biosynthesis, and cell death. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs), which transfer ADP-ribose from NAD+ onto substrates. The modification, which occurs as mono- or poly-ADP-ribosylation, is reversible due to the action of different ADP-ribosylhydrolases. Importantly, inhibitors of ARTs are approved or are being developed for clinical use. Moreover, ADP-ribosylhydrolases are being assessed as therapeutic targets, foremost as antiviral drugs and for oncological indications. Due to the development of novel reagents and major technological advances that allow the study of ADP-ribosylation in unprecedented detail, an increasing number of cellular processes and pathways are being identified that are regulated by ADP-ribosylation. In addition, characterization of biochemical and structural aspects of the ARTs and their catalytic activities have expanded our understanding of this protein family. This increased knowledge requires that a common nomenclature be used to describe the relevant enzymes. Therefore, in this viewpoint, we propose an updated and broadly supported nomenclature for mammalian ARTs that will facilitate future discussions when addressing the biochemistry and biology of ADP-ribosylation. This is combined with a brief description of the main functions of mammalian ARTs to illustrate the increasing diversity of mono- and poly-ADP-ribose mediated cellular processes.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Peter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Hungary
| | | | - Michael Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Daniela Corda
- Department of Biomedical Sciences, National Research Council, Rome, Italy
| | | | - Matthew D Daugherty
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Anthony R Fehr
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | | | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | | | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Nicolas C Hoch
- Department of Biochemistry, University of São Paulo, Brazil
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Ladurner
- Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Germany
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, Norway
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joel Moss
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Friedrich Nolte
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Germany
| | - John Pascal
- Biochemistry and Molecular Medicine, Université de Montréal, Canada
| | - Bryce M Paschal
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, NY, USA
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller University of Jena, Germany
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Roko Zaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
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16
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Thomas A, Fontaine SD, Diolaiti ME, Desai P, Kumar R, Takahashi N, Sciuto L, Nichols S, Ashworth A, Feng FY, Ashley GW, Nguyen M, Pommier Y, Santi DV. PLX038: A Long-Acting Topoisomerase I Inhibitor With Robust Antitumor Activity in ATM-Deficient Tumors and Potent Synergy With PARP Inhibitors. Mol Cancer Ther 2022; 21:1722-1728. [PMID: 35999657 PMCID: PMC10673686 DOI: 10.1158/1535-7163.mct-22-0217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/02/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Alterations in the ATM gene are among the most common somatic and hereditary cancer mutations, and ATM-deficient tumors are hypersensitive to DNA-damaging agents. A synthetic lethal combination of DNA-damaging agents and DNA repair inhibitors could have widespread utility in ATM-deficient cancers. However, overlapping normal tissue toxicities from these drug classes have precluded their clinical translation. We investigated PLX038, a releasable polyethylene glycol-conjugate of the topoisomerase I inhibitor SN-38, in ATM wild-type and null isogenic xenografts and in a BRCA1-deficient xenograft. PLX038 monotherapy and combination with PARP inhibition potently inhibited the growth of both BRCA1- and ATM-deficient tumors. A patient with an ATM-mutated breast cancer treated with PLX038 and the PARP inhibitor rucaparib achieved rapid, symptomatic, and radiographic complete response lasting 12 months. Single-agent PLX038 or PLX038 in combination with DNA damage response inhibitors are novel therapeutic paradigms for patients with ATM-loss cancers.
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Affiliation(s)
| | | | - Morgan E. Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | | | | | | | | | | | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Felix Y. Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
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17
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Sjöström M, Zhao SG, Levy S, Zhang M, Ning Y, Shrestha R, Lundberg A, Herberts C, Foye A, Aggarwal R, Hua JT, Li H, Bergamaschi A, Maurice-Dror C, Maheshwari A, Chen S, Ng SWS, Ye W, Petricca J, Fraser M, Chesner L, Perry MD, Moreno-Rodriguez T, Chen WS, Alumkal JJ, Chou J, Morgans AK, Beer TM, Thomas GV, Gleave M, Lloyd P, Phillips T, McCarthy E, Haffner MC, Zoubeidi A, Annala M, Reiter RE, Rettig MB, Witte ON, Fong L, Bose R, Huang FW, Luo J, Bjartell A, Lang JM, Mahajan NP, Lara PN, Evans CP, Tran PT, Posadas EM, He C, Cui XL, Huang J, Zwart W, Gilbert LA, Maher CA, Boutros PC, Chi KN, Ashworth A, Small EJ, He HH, Wyatt AW, Quigley DA, Feng FY. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer. Cancer Res 2022; 82:3888-3902. [PMID: 36251389 PMCID: PMC9627125 DOI: 10.1158/0008-5472.can-22-1123] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Abstract
Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease. SIGNIFICANCE In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
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Affiliation(s)
- Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Oncology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI
- William S. Middleton Memorial Veterans' Hospital, Madison, WI
| | | | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | | | - Corinne Maurice-Dror
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver, BC, Canada
| | - Ashutosh Maheshwari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Sujun Chen
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wenbin Ye
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Automation, Xiamen University, Xiamen, Fujian, China
| | - Jessica Petricca
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Lisa Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marc D Perry
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - William S Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Alicia K Morgans
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - George V Thomas
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- University of Washington, Seattle, WA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Robert E Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
| | - Matthew B Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Anders Bjartell
- Department of Translational Medicine, Medical Faculty, Lund University, Malmö, Sweden
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin-Madison, Madison, WI
| | | | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA
- Department of Urologic Surgery, University of California Davis, Sacramento, CA
| | - Phuoc T Tran
- Department of Radiation Oncology, University of Maryland, College Park, Baltimore, MD
| | - Edwin M Posadas
- Urologic Oncology Program & Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Arc Institute, Palo Alto, CA
| | - Christopher A Maher
- Siteman Cancer Center, Washington University, St. Louis, MO
- McDonnell Genome Institute, Washington University, St. Louis, MO
- Department of Internal Medicine, Washington University, St. Louis, MO
- Department of Biomedical Engineering, Washington University, St. Louis, MO
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA
- Jonsson Comprehensive Cancer Center, Departments of Human Genetics and Urology, University of California Los Angeles, Los Angeles, CA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA
- Department of Urology, University of California, San Francisco, San Francisco, CA
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18
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Warthi G, Faulkner JL, Doja J, Ghanam AR, Gao P, Yang AC, Slivano OJ, Barris CT, Kress TC, Zawieja SD, Griffin SH, Xie X, Ashworth A, Christie CK, Bryant WB, Kumar A, Davis MJ, Long X, Gan L, de Chantemèle EJB, Lyu Q, Miano JM. Generation and Comparative Analysis of an Itga8-CreER T2 Mouse with Preferential Activity in Vascular Smooth Muscle Cells. Nat Cardiovasc Res 2022; 1:1084-1100. [PMID: 36424917 PMCID: PMC9681021 DOI: 10.1038/s44161-022-00162-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022]
Abstract
All current smooth muscle cell (SMC) Cre mice similarly recombine floxed alleles in vascular and visceral SMCs. Here, we present an Itga8-CreER T2 knock-in mouse and compare its activity with a Myh11-CreER T2 mouse. Both Cre drivers demonstrate equivalent recombination in vascular SMCs. However, Myh11-CreER T2 mice, but not Itga8-CreER T2 mice, display high activity in visceral SMC-containing tissues such as intestine, show early tamoxifen-independent activity, and produce high levels of CreERT2 protein. Whereas Myh11-CreER T2 -mediated knockout of serum response factor (Srf) causes a lethal intestinal phenotype precluding analysis of the vasculature, loss of Srf with Itga8-CreER T2 (Srf Itga8 ) yields viable mice with no evidence of intestinal pathology. Male and female Srf Itga8 mice exhibit vascular contractile incompetence, and angiotensin II causes elevated blood pressure in wild type, but not Srf Itga8 , male mice. These findings establish the Itga8-CreER T2 mouse as an alternative to existing SMC Cre mice for unfettered phenotyping of vascular SMCs following selective gene loss.
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Affiliation(s)
- Ganesh Warthi
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Jessica L. Faulkner
- Department of Physiology, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Jaser Doja
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Amr R. Ghanam
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Pan Gao
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Allison C. Yang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Orazio J. Slivano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Candee T. Barris
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Taylor C. Kress
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Scott D. Zawieja
- Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Susan H. Griffin
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Xiaoling Xie
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158
| | - Christine K. Christie
- Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - William B. Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Ajay Kumar
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Michael J. Davis
- Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | - Lin Gan
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
| | | | - Qing Lyu
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
- Biomedical and Health Institute, Chongqing Institute of Green and Intelligence Technology, Chongqing, China 400714
- Chongqing General Hospital, Chongqing, China 401147
| | - Joseph M. Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia 30912
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19
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O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A. Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2. Cancer Res 2022; 82:3950-3961. [PMID: 36273492 PMCID: PMC9633439 DOI: 10.1158/0008-5472.can-21-4335] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/20/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
Abstract
Over one million cases of gastric cancer are diagnosed each year globally, and the metastatic disease continues to have a poor prognosis. A significant proportion of gastric tumors have defects in the DNA damage response pathway, creating therapeutic opportunities through synthetic lethal approaches. Several small-molecule inhibitors of ATR, a key regulator of the DNA damage response, are now in clinical development as targeted agents for gastric cancer. Here, we performed a large-scale CRISPR interference screen to discover genetic determinants of response and resistance to ATR inhibitors (ATRi) in gastric cancer cells. Among the top hits identified as mediators of ATRi response were UPF2 and other components of the nonsense-mediated decay (NMD) pathway. Loss of UPF2 caused ATRi resistance across multiple gastric cancer cell lines. Global proteomic, phosphoproteomic, and transcriptional profiling experiments revealed that cell-cycle progression and DNA damage responses were altered in UPF2-mutant cells. Further studies demonstrated that UPF2-depleted cells failed to accumulate in G1 following treatment with ATRi. UPF2 loss also reduced transcription–replication collisions, which has previously been associated with ATRi response, thereby suggesting a possible mechanism of resistance. Our results uncover a novel role for NMD factors in modulating response to ATRi in gastric cancer, highlighting a previously unknown mechanism of resistance that may inform the clinical use of these drugs.
Significance:
Loss of NMD proteins promotes resistance to ATR inhibitors in gastric cancer cells, which may provide a combination of therapeutic targets and biomarkers to improve the clinical utility of these drugs.
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Affiliation(s)
- Patrick C. O'Leary
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Huadong Chen
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Yagmur U. Doruk
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Tess Williamson
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Benjamin Polacco
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Andrew S. McNeal
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Tanushree Shenoy
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Nupura Kale
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Julia Carnevale
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
- 5Department of Medicine, University of California San Francisco, San Francisco, California
| | - Erica Stevenson
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - David A. Quigley
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 6Department of Urology, University of California San Francisco, San Francisco, California
- 7Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 5Department of Medicine, University of California San Francisco, San Francisco, California
| | - Felix Y. Feng
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 6Department of Urology, University of California San Francisco, San Francisco, California
- 8Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Danielle L. Swaney
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Nevan J. Krogan
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Minkyu Kim
- 2Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California
- 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- 4Gladstone Institutes, San Francisco, California
| | - Morgan E. Diolaiti
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Alan Ashworth
- 1UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- 5Department of Medicine, University of California San Francisco, San Francisco, California
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Carnevale J, Shifrut E, Kale N, Nyberg WA, Blaeschke F, Chen YY, Li Z, Bapat SP, Diolaiti ME, O'Leary P, Vedova S, Belk J, Daniel B, Roth TL, Bachl S, Anido AA, Prinzing B, Ibañez-Vega J, Lange S, Haydar D, Luetke-Eversloh M, Born-Bony M, Hegde B, Kogan S, Feuchtinger T, Okada H, Satpathy AT, Shannon K, Gottschalk S, Eyquem J, Krenciute G, Ashworth A, Marson A. RASA2 ablation in T cells boosts antigen sensitivity and long-term function. Nature 2022; 609:174-182. [PMID: 36002574 PMCID: PMC9433322 DOI: 10.1038/s41586-022-05126-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 07/20/2022] [Indexed: 12/17/2022]
Abstract
The efficacy of adoptive T cell therapies for cancer treatment can be limited by suppressive signals from both extrinsic factors and intrinsic inhibitory checkpoints1,2. Targeted gene editing has the potential to overcome these limitations and enhance T cell therapeutic function3-10. Here we performed multiple genome-wide CRISPR knock-out screens under different immunosuppressive conditions to identify genes that can be targeted to prevent T cell dysfunction. These screens converged on RASA2, a RAS GTPase-activating protein (RasGAP) that we identify as a signalling checkpoint in human T cells, which is downregulated upon acute T cell receptor stimulation and can increase gradually with chronic antigen exposure. RASA2 ablation enhanced MAPK signalling and chimeric antigen receptor (CAR) T cell cytolytic activity in response to target antigen. Repeated tumour antigen stimulations in vitro revealed that RASA2-deficient T cells show increased activation, cytokine production and metabolic activity compared with control cells, and show a marked advantage in persistent cancer cell killing. RASA2-knockout CAR T cells had a competitive fitness advantage over control cells in the bone marrow in a mouse model of leukaemia. Ablation of RASA2 in multiple preclinical models of T cell receptor and CAR T cell therapies prolonged survival in mice xenografted with either liquid or solid tumours. Together, our findings highlight RASA2 as a promising target to enhance both persistence and effector function in T cell therapies for cancer treatment.
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Affiliation(s)
- Julia Carnevale
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA.
| | - Eric Shifrut
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- The School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
- Department of Pathology Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Varda and Boaz Dotan Center for Advanced Therapies, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
| | - Nupura Kale
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - William A Nyberg
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Yan Yi Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Sagar P Bapat
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Morgan E Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick O'Leary
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Shane Vedova
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Julia Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Theodore L Roth
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Stefanie Bachl
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Alejandro Allo Anido
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brooke Prinzing
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jorge Ibañez-Vega
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shannon Lange
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Marie Luetke-Eversloh
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Maelys Born-Bony
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Bindu Hegde
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Scott Kogan
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tobias Feuchtinger
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Dr von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Hideho Okada
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA
| | - Kevin Shannon
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
| | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Alan Ashworth
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko D, Moroz Y, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2. bioRxiv 2022:2022.06.27.497816. [PMID: 35794891 PMCID: PMC9258288 DOI: 10.1101/2022.06.27.497816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 152 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated protein dynamics within the active site, and key inhibitor motifs that will template future drug development against Mac1.
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Affiliation(s)
- Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Yagmur Umay Doruk
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Moira Rachman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Siyi Wang
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Dmytro Radchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Yurii Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Chemspace, Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adam R. Renslo
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA
| | - Jenny C. Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
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23
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Belk JA, Yao W, Ly N, Freitas KA, Chen YT, Shi Q, Valencia AM, Shifrut E, Kale N, Yost KE, Duffy CV, Daniel B, Hwee MA, Miao Z, Ashworth A, Mackall CL, Marson A, Carnevale J, Vardhana SA, Satpathy AT. Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. Cancer Cell 2022; 40:768-786.e7. [PMID: 35750052 PMCID: PMC9949532 DOI: 10.1016/j.ccell.2022.06.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 11/29/2022]
Abstract
T cell exhaustion limits antitumor immunity, but the molecular determinants of this process remain poorly understood. Using a chronic stimulation assay, we performed genome-wide CRISPR-Cas9 screens to systematically discover regulators of T cell exhaustion, which identified an enrichment of epigenetic factors. In vivo CRISPR screens in murine and human tumor models demonstrated that perturbation of the INO80 and BAF chromatin remodeling complexes improved T cell persistence in tumors. In vivo Perturb-seq revealed distinct transcriptional roles of each complex and that depletion of canonical BAF complex members, including Arid1a, resulted in the maintenance of an effector program and downregulation of exhaustion-related genes in tumor-infiltrating T cells. Finally, Arid1a depletion limited the acquisition of exhaustion-associated chromatin accessibility and led to improved antitumor immunity. In summary, we provide an atlas of the genetic regulators of T cell exhaustion and demonstrate that modulation of epigenetic state can improve T cell responses in cancer immunotherapy.
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Affiliation(s)
- Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Winnie Yao
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Nghi Ly
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Katherine A Freitas
- Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA 94035, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94035, USA
| | - Yan-Ting Chen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Quanming Shi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alfredo M Valencia
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Eric Shifrut
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Nupura Kale
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kathryn E Yost
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Connor V Duffy
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Zhuang Miao
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Crystal L Mackall
- Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Division of Pediatric Hematology/Oncology/Stem Cell Transplant and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94035, USA; Division of BMT and Cell Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94035, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Julia Carnevale
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Santosh A Vardhana
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA 94035, USA; Parker Institute of Cancer Immunotherapy, San Francisco, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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24
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Chen H, Diolaiti ME, O’Leary PC, Rojc A, Krogan NJ, Kim M, Ashworth A. A Whole-Genome CRISPR Screen Identifies AHR Loss as a Mechanism of Resistance to a PARP7 Inhibitor. Mol Cancer Ther 2022; 21:1076-1089. [PMID: 35439318 PMCID: PMC9769698 DOI: 10.1158/1535-7163.mct-21-0841] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/09/2022] [Accepted: 04/12/2022] [Indexed: 01/07/2023]
Abstract
Inhibitors directed toward PARP1 and PARP2 are approved agents for the treatment of BRCA1 and BRCA2-related cancers. Other members of the PARP family have also been implicated in cancer and are being assessed as therapeutic targets in cancer and other diseases. Recently, an inhibitor of PARP7 (RBN-2397) has reached early-stage human clinical trials. Here, we performed a genome-wide CRISPR screen for genes that modify the response of cells to RBN-2397. We identify the polycyclic aromatic hydrocarbon receptor AHR and multiple components of the cohesin complex as determinants of resistance to this agent. Activators and inhibitors of AHR modulate the cellular response to PARP7 inhibition, suggesting potential combination therapy approaches.
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Affiliation(s)
- Huadong Chen
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA 94158
| | - Morgan E. Diolaiti
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA 94158
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Patrick C. O’Leary
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA 94158
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Ajda Rojc
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA 94158
- The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA 94158
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA 94158
- The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA 94158
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Minkyu Kim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA 94158
- The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA 94158
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA 94158
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA 94158
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
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25
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Sci Adv 2022; 8:eabo5083. [PMID: 35622909 PMCID: PMC9140965 DOI: 10.1126/sciadv.abo5083] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 05/04/2023]
Abstract
The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
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26
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Byrnes JR, Weeks AM, Shifrut E, Carnevale J, Kirkemo L, Ashworth A, Marson A, Wells JA. Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression. Mol Cell Proteomics 2022; 21:100217. [PMID: 35217172 PMCID: PMC9006863 DOI: 10.1016/j.mcpro.2022.100217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 01/02/2023] Open
Abstract
Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the antitumor immune response. T cell surface receptors and surface proteins that influence interactions and function in the TME are proven targets for cancer immunotherapy. However, how the entire surface proteome remodels in primary human T cells in response to specific suppressive factors in the TME remains to be broadly and systematically characterized. Here, using a reductionist cell culture approach with primary human T cells and stable isotopic labeling with amino acids in cell culture–based quantitative cell surface capture glycoproteomics, we examined how two immunosuppressive TME factors, regulatory T cells (Tregs) and hypoxia, globally affect the activated CD8+ surface proteome (surfaceome). Surprisingly, coculturing primary CD8+ T cells with Tregs only modestly affected the CD8+ surfaceome but did partially reverse activation-induced surfaceomic changes. In contrast, hypoxia drastically altered the CD8+ surfaceome in a manner consistent with both metabolic reprogramming and induction of an immunosuppressed state. The CD4+ T cell surfaceome similarly responded to hypoxia, revealing a common hypoxia-induced surface receptor program. Our surfaceomics findings suggest that hypoxic environments create a challenge for T cell activation. These studies provide global insight into how Tregs and hypoxia remodel the T cell surfaceome and we believe represent a valuable resource to inform future therapeutic efforts to enhance T cell function. Quantitative surface proteomics of primary human T cells Activation, regulatory T cells, and hypoxia induce bidirectional surfaceome changes Hypoxia dramatically remodels the primary T cell surface proteome Both regulatory T cells and hypoxia downregulate nutrient transporter expression
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Affiliation(s)
- James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA; Gladstone Institutes, San Francisco, California, USA
| | - Julia Carnevale
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lisa Kirkemo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Alan Ashworth
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA; The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA; Gladstone Institutes, San Francisco, California, USA; Department of Medicine, University of California, San Francisco, San Francisco, California, USA; The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA; Parker Institute for Cancer Immunotherapy, San Francisco, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.
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27
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Hiatt RA, Sibley A, Venkatesh B, Cheng J, Dixit N, Fox R, Ling P, Nguyen T, Oh D, Palmer NR, Pasick RJ, Potter MB, Somsouk M, Vargas RA, Vijayaraghavan M, Ashworth A. From Cancer Epidemiology to Policy and Practice: the Role of a Comprehensive Cancer Center. CURR EPIDEMIOL REP 2022; 9:10-21. [PMID: 35342686 PMCID: PMC8935108 DOI: 10.1007/s40471-021-00280-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
Purpose of Review Cancer incidence and mortality are decreasing, but inequities in outcomes persist. This paper describes the San Francisco Cancer Initiative (SF CAN) as a model for the systematic application of epidemiological evidence to reduce the cancer burden and associated inequities. Recent Findings SF CAN is a multi-institutional implementation of existing evidence on the prevention and early detection of five common cancers (i.e., breast, prostate, colorectal, liver, and lung/tobacco-related cancers) accounting for 50% of cancer deaths in San Francisco. Five Task Forces follow individual logic models designating inputs, outputs, and outcomes. We describe the progress made and the challenges faced by each Task Force after 5 years of activity. Summary SF CAN is a model for how the nation’s Comprehensive Cancer Centers are ideally positioned to leverage cancer epidemiology for evidence-based initiatives that, along with genuine community engagement and multiple stakeholders, can reduce the population burden of cancer.
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Affiliation(s)
- Robert A Hiatt
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, USA.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, USA.,Mission Hall UCSF, 550 16th Street, 2nd Floor, San Francisco, CA 94158 USA
| | - Amanda Sibley
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, USA
| | - Brinda Venkatesh
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, USA
| | - Joyce Cheng
- Chinese Community Health Resource Center, San Francisco, USA
| | - Niharika Dixit
- Division of Hematology/Oncology, UCSF at Zuckerberg San Francisco General Hospital, San Francisco, USA
| | - Rena Fox
- Department of Medicine, UCSF, San Francisco, USA
| | - Pamela Ling
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, USA.,Department of Medicine, UCSF, San Francisco, USA.,Center for Tobacco Control Research and Education, UCSF, San Francisco, USA
| | - Tung Nguyen
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, USA.,Department of Medicine, UCSF, San Francisco, USA
| | - Debora Oh
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, USA
| | | | | | - Michael B Potter
- Department of Family and Community Medicine, UCSF, San Francisco, USA
| | - Ma Somsouk
- Division of Gastroenterology, UCSF, San Francisco, USA
| | - Roberto Ariel Vargas
- Center for Community Engagement, UCSF, San Francisco, USA.,Clinical and Translational Science Institute, UCSF, San Francisco, USA
| | | | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, USA
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28
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Im SA, Lee KH, Min A, Lee D, Kim TY, Ryu HS, Koh J, Cheon GJ, Shin YJ, Kim Y, Moon HG, Han W, Lee HB, Diolaiti M, Quigley D, Ashworth A, Cho N. Abstract PD15-08: Window of opportunity trial of neoadjuvant olaparib and durvalumab for triple negative or low ER-positive breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-pd15-08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background PARP inhibitors have proven efficacy in breast cancer patients with germline BRCA1 or BRCA2 mutations (gBRCAmt) but also have potential to be effective in cancers with defects in homologous recombination (HR) DNA repair. Moreover, synergy between PARP inhibition and immune checkpoint blockade is expected based on increased mutation burden, neoantigen expression, and immunogenic cell death. Triple negative breast cancer (TNBC) or low estrogen receptor (ER)-positive breast cancers may have diverse defects in HR repair. Methods This is a window of opportunity, serial biopsy trial of olaparib and durvalumab before standard neoadjuvant chemotherapy for TNBC or low ER+ breast cancer (NCT03594396). Patients had clinical stage II/III TNBC or low ER+ HER2- breast cancers where ER was expressed in 10% or lower in tumor cells. Olaparib 300mg bid was given for 4 weeks without rest. One dose of durvalumab 1500mg was given on day 15. Study tumor biopsy and blood sample were taken before the study treatment, after 2 weeks of olaparib before durvalumab, and 2 weeks after durvalumab at the completion of 4 weeks of olaparib. FDG-PET/MRI was taken at baseline, after 2 weeks, after 4 weeks of study treatment, and computed tomography (CT) scan at baseline and after 4 weeks. After the study treatment, standard neoadjuvant chemotherapy with 4 cycles of doxorubicin+cyclophosphamide followed by 4 cycles of docetaxel was given. Primary endpoint was the changes of tumor biology detected by serial tumor biopsy. Secondary endpoints were pathological complete response (pCR) rate, response rate, prediction of early metabolic response by functional HR status, and safety. Functional HR deficiency was assessed by counting RAD51 foci as a marker for HR repair in the baseline tumor tissues before and after 30Gy irradiation to induce DNA damage. Results Fifty-four female patients were enrolled (median age 40 years, range 24-68). ER was negative (TNBC) in 43 patients and low-positive in 11 patients. Clinical stage was II in 25 patients and III in 29 patients, and axillary lymph node involvement was in 47 patients. gBRCAmt was assessed in 53 patients and 16 (30.1%) harbored pathogenic mutations. Functional HR status as measured by RAD51 foci formation was deficient in 27 (50%) patients and proficient in 27 (50%) patients. Functional HR deficiency was related with early metabolic response by FDG-PET after 2 weeks of olaparib (response in 17/27 HR-deficient tumors [63.0%] vs. 7/27 HR-proficient tumors [25.9%]; p=.006). After 4 weeks of olaparib and durvalumab, HR-deficiency was still related to metabolic response (23/27 vs. 17/27, respectively; p=.062) but HR-proficient tumors also showed metabolic decline. Moreover, HR deficiency was also related with RECIST response measured by CT after 4 weeks (17/27 vs. 9/27; p=.029). As of June 2021, 40 patients completed the neoadjuvant treatment and surgery; among those, 30 achieved pCR (pCR rate 75%). Among 13 patients with gBRCAmt who underwent surgery, 11 achieved pCR (84.6%). Updated results on pCR will be presented. Conclusions Olaparib and durvalumab followed by standard neoadjuvant chemotherapy shows very high pCR rate in TNBC or low ER+ stage II/III breast cancer. Functional HR status as measured by RAD51 foci formation was predictive of early metabolic response to olaparib. Genomic and transcriptomic analyses are underway in the samples before, during, and after olaparib and durvalumab.
Citation Format: Seock-Ah Im, Kyung-Hun Lee, Ahrum Min, Daewon Lee, Tae Yong Kim, Han Suk Ryu, Jiwon Koh, Gi-Jeong Cheon, Yoon-Jung Shin, Yujin Kim, Hyeong-Gon Moon, Wonshik Han, Han-Byoel Lee, Morgan Diolaiti, David Quigley, Alan Ashworth, Nariya Cho. Window of opportunity trial of neoadjuvant olaparib and durvalumab for triple negative or low ER-positive breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD15-08.
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Affiliation(s)
- Seock-Ah Im
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Kyung-Hun Lee
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Ahrum Min
- Cancer Research Institute, Seoul National University, Seoul, Korea, Republic of
| | - Daewon Lee
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Tae Yong Kim
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Han Suk Ryu
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Jiwon Koh
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Gi-Jeong Cheon
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Yoon-Jung Shin
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Yujin Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea, Republic of
| | - Hyeong-Gon Moon
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Wonshik Han
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Han-Byoel Lee
- Seoul National University Hospital, Seoul, Korea, Republic of
| | - Morgan Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - David Quigley
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Nariya Cho
- Seoul National University Hospital, Seoul, Korea, Republic of
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29
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. bioRxiv 2022:2022.02.07.479477. [PMID: 35169801 PMCID: PMC8845425 DOI: 10.1101/2022.02.07.479477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
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30
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Guix I, Liu Q, Pujana MA, Ha P, Piulats J, Linares I, Guedea F, Mao JH, Lazar A, Chapman J, Yom SS, Ashworth A, Barcellos-Hoff MH. Validation of anti-correlated TGFβ signaling and alternative end-joining DNA repair signatures that predict response to genotoxic cancer therapy. Clin Cancer Res 2022; 28:1372-1382. [PMID: 35022323 DOI: 10.1158/1078-0432.ccr-21-2846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/13/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Loss of transforming growth factor β (TGFβ) signaling increases error-prone alternative end-joining (alt-EJ) DNA repair. We previously translated this mechanistic relationship as TGFβ and alt-EJ gene expression signatures, which are anti-correlated across cancer types. A score, βAlt, representing anti-correlation predicts patient outcome in response to genotoxic therapy. Here we sought to verify this biology in live specimens and additional datasets. EXPERIMENTAL DESIGN Human head and neck squamous cell (HNSC) carcinoma explants were treated in vitro to test whether the signatures report TGFβ signaling, indicated by SMAD2 phosphorylation, and unrepaired DNA damage, indicated by persistent 53BP1 foci after irradiation or olaparib. A custom NanoString assay was implemented to analyze the signatures' expression in explants. Each signature gene was then weighted by its association with functional responses to define a modified score, βAltw, that was retested for association with response to genotoxic therapies in independent datasets. RESULTS Most genes in each signature were positively correlated with the expected biological response in tumor explants. Anticorrelation of TGFβ and alt-EJ signatures measured by Nanostring was confirmed in explants. βAltw was significantly (P<0.001) better than βAlt in predicting overall survival in response to genotoxic therapy in TCGA pancancer patients and in independent HNSC and ovarian cancer patient datasets. CONCLUSION Association of the TGFβ and alt-EJ signatures with their biological response validates TGFβ competency as a key mediator of DNA repair that can be readily assayed by gene expression. The predictive value of βAltw supports its development to assist in clinical decision-making.
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Affiliation(s)
- Ines Guix
- Department of Radiation Oncology, University of California, San Francicsco
| | - Qi Liu
- Shenzhen Bay Laboratory, Institute for Biomedical Engineering
| | | | - Patrick Ha
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco
| | - Josep Piulats
- Medical Oncology, Institut Català d'Oncologia-IDIBELL
| | | | | | - Jian-Hua Mao
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, University of California, Berkely
| | - Ann Lazar
- Biostatistics, University of California, San Francisco
| | - Jocelyn Chapman
- Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco
| | - Sue S Yom
- Radiation Oncology, University of California, San Francisco
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Centre
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31
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Yan M, Sigurdson S, Greifer N, Kennedy T, Toh T, Jr PL, Weiss J, Hueniken K, Yeung C, Sugumar V, Sun A, Bezjak A, Cho J, Raman S, Hope A, Giuliani M, Stuart E, Owen T, Ashworth A, Robinson A, Liu G, Moraes F, Lok B. A Comparison of Hypofractionated and Twice Daily Thoracic Irradiation in Limited-Stage Small Cell Lung Cancer: An Overlap Weighted Analysis. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van 't Veer L, Ashworth A, Ideker T, Krogan NJ. A protein interaction landscape of breast cancer. Science 2021; 374:eabf3066. [PMID: 34591612 PMCID: PMC9040556 DOI: 10.1126/science.abf3066] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Minkyu Kim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Jisoo Park
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Mehdi Bouhaddou
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Kyumin Kim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Ajda Rojc
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Margaret Soucheray
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Michael J McGregor
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Patrick O'Leary
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Denise Wolf
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Erica Stevenson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Dominique Mitchell
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Kari A Herrington
- Department of Biochemistry and Biophysics, Center for Advanced Light Microscopy, University of California, San Francisco, CA, USA
| | - Denise P Muñoz
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Kuei-Ho Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Fan Zheng
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Jason F Kreisberg
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Morgan E Diolaiti
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - John D Gordan
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Jean-Philippe Coppé
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Laura van 't Veer
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Alan Ashworth
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Trey Ideker
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA.,Department of Bioengineering, University of California, San Diego, CA, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
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33
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Monk EJM, Rautemaa-Richardson R, Felton T, Montalti A, Parkes M, Templeton R, Ashworth A, Garcia M, Barker J, Thomas S. Candidaemia incidence in prolonged veno-venous extracorporeal membrane oxygenation. J Hosp Infect 2021; 119:49-53. [PMID: 34562545 DOI: 10.1016/j.jhin.2021.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 11/25/2022]
Abstract
This single-centre retrospective study reports the dynamics of candida bloodstream infection (CBSI) incidence in 145 patients receiving venovenous ECMO for respiratory support, between January 2014 and December 2018. Incidence rate and odds ratio (OR) of CBSI were calculated, stratified by week of ECMO exposure. Weekly incidence increased throughout the ECMO run, with a rising trend in OR (P = 0.005), and a window of continued risk after decannulation was observed. Of the 13 patients that developed CBSI, five (38%) received empirical micafungin treatment before positive culture due to clinical suspicion. Prospective studies, aiming to improve ECMO diagnostic stewardship practices and discourage antifungal prophylaxis or empiric management where unnecessary, are needed.
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Affiliation(s)
- Edward J M Monk
- Department of Microbiology, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom; Infectious Diseases Service, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom.
| | - Riina Rautemaa-Richardson
- Infectious Diseases Service, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom; Mycology Reference Centre Manchester (ECMM Centre of Excellence), Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom; Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Timothy Felton
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom; Acute Intensive Care Unit, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom; Department of Respiratory Medicine, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
| | - Alice Montalti
- Cardiothoracic Critical Care Unit, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
| | - Matthew Parkes
- Centre for Biostatistics, Faculty of Biology, Medicine and Health, University of Manchester, United Kingdom
| | - Richard Templeton
- Cardiothoracic Critical Care Unit, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
| | - Alan Ashworth
- Cardiothoracic Critical Care Unit, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
| | - Miguel Garcia
- Cardiothoracic Critical Care Unit, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
| | - Julian Barker
- Cardiothoracic Critical Care Unit, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
| | - Stephanie Thomas
- Department of Microbiology, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
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34
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Das R, Sjöström M, Shrestha R, Yogodzinski C, Egusa EA, Chesner LN, Chen WS, Chou J, Dang DK, Swinderman JT, Ge A, Hua JT, Kabir S, Quigley DA, Small EJ, Ashworth A, Feng FY, Gilbert LA. An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer. Nat Commun 2021; 12:4601. [PMID: 34326322 PMCID: PMC8322386 DOI: 10.1038/s41467-021-24919-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
Genomic sequencing of thousands of tumors has revealed many genes associated with specific types of cancer. Similarly, large scale CRISPR functional genomics efforts have mapped genes required for cancer cell proliferation or survival in hundreds of cell lines. Despite this, for specific disease subtypes, such as metastatic prostate cancer, there are likely a number of undiscovered tumor specific driver genes that may represent potential drug targets. To identify such genetic dependencies, we performed genome-scale CRISPRi screens in metastatic prostate cancer models. We then created a pipeline in which we integrated pan-cancer functional genomics data with our metastatic prostate cancer functional and clinical genomics data to identify genes that can drive aggressive prostate cancer phenotypes. Our integrative analysis of these data reveals known prostate cancer specific driver genes, such as AR and HOXB13, as well as a number of top hits that are poorly characterized. In this study we highlight the strength of an integrated clinical and functional genomics pipeline and focus on two top hit genes, KIF4A and WDR62. We demonstrate that both KIF4A and WDR62 drive aggressive prostate cancer phenotypes in vitro and in vivo in multiple models, irrespective of AR-status, and are also associated with poor patient outcome.
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Affiliation(s)
- Rajdeep Das
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Yogodzinski
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Emily A Egusa
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lisa N Chesner
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - William S Chen
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Donna K Dang
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jason T Swinderman
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Alex Ge
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Shaheen Kabir
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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35
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Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, O'Leary P, Wolf D, Mitchell DC, Zheng F, Gordan JD, Coppé JP, Swaney DL, van' t Veer L, Ashworth A, Ideker T, Krogan NJ. Abstract 2308: The protein interaction landscape of breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancers have been associated with a diverse array of genomic alterations, many of which are rare with unknown significance. To understand the cellular mechanisms impacted by such alterations in breast invasive carcinoma, we have applied affinity-purification mass spectrometry to delineate comprehensive biophysical interaction networks for 40 frequently altered breast cancer proteins across three human breast cell lines, providing a novel resource of context-specific and shared protein-protein interaction networks in breast cancer cells. These networks interconnect and enrich for common and rare cancer mutations, and are substantially rewired by mutations. Our analysis identifies novel PIK3CA-interacting proteins which repress AKT signaling, and UBE2N emerges as a BRCA1 interactor predictive of clinical response to PARP inhibition. We also show that Spinophilin interacts with and dephosphorylates BRCA1 to promote DNA double-strand break repair. Thus, cancer protein interaction landscapes provide a framework for recognizing oncogenic drivers and drug vulnerabilities.
Citation Format: Minkyu Kim, Jisoo Park, Mehdi Bouhaddou, Kyumin Kim, Ajda Rojc, Maya Modak, Margaret Soucheray, Patrick O'Leary, Denise Wolf, Dominique C. Mitchell, Fan Zheng, John D. Gordan, Jean-Philippe Coppé, Danielle L. Swaney, Laura van' t Veer, Alan Ashworth, Trey Ideker, Nevan J. Krogan. The protein interaction landscape of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2308.
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Affiliation(s)
- Minkyu Kim
- 1University of California San Francisco, San Francisco, CA
| | - Jisoo Park
- 2University of California San Diego, San Diego, CA
| | | | - Kyumin Kim
- 3University of Southern California, Los Angeles, CA
| | - Ajda Rojc
- 1University of California San Francisco, San Francisco, CA
| | - Maya Modak
- 1University of California San Francisco, San Francisco, CA
| | | | | | - Denise Wolf
- 1University of California San Francisco, San Francisco, CA
| | | | - Fan Zheng
- 2University of California San Diego, San Diego, CA
| | - John D. Gordan
- 1University of California San Francisco, San Francisco, CA
| | | | | | | | - Alan Ashworth
- 1University of California San Francisco, San Francisco, CA
| | - Trey Ideker
- 2University of California San Diego, San Diego, CA
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36
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Abstract
A phase I study defined a tolerable combination of the ATR inhibitor ceralasertib with paclitaxel and responses were seen in patients with melanoma who had progressed on an immune checkpoint inhibitor. This combination warrants further exploration to determine the extent and molecular determinants of clinical activity.See related article by Kim et al., p. 4700.
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Affiliation(s)
- Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California.
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37
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Maguire S, Perraki E, Tomczyk K, Jones ME, Fletcher O, Pugh M, Winter T, Thompson K, Cooke R, Trainer A, James P, Bojesen S, Flyger H, Nevanlinna H, Mattson J, Friedman E, Laitman Y, Palli D, Masala G, Zanna I, Ottini L, Silvestri V, Hollestelle A, Hooning MJ, Novaković S, Krajc M, Gago-Dominguez M, Castelao JE, Olsson H, Hedenfalk I, Saloustros E, Georgoulias V, Easton DF, Pharoah P, Dunning AM, Bishop DT, Neuhausen SL, Steele L, Ashworth A, Garcia Closas M, Houlston R, Swerdlow A, Orr N. Common Susceptibility Loci for Male Breast Cancer. J Natl Cancer Inst 2021; 113:453-461. [PMID: 32785646 PMCID: PMC8023850 DOI: 10.1093/jnci/djaa101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC. METHODS We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10-06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided. RESULTS The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10-08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor-positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10-30). CONCLUSIONS These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.
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Affiliation(s)
- Sarah Maguire
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Eleni Perraki
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Katarzyna Tomczyk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Matthew Pugh
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Timothy Winter
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Kyle Thompson
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - kConFab Consortium
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Trainer
- Parkville Familial Cancer Clinic, Sir Peter MacCallum Department of Oncology, University of Melbourne and Royal Melbourne Hospital, East Melbourne, Victoria, Australia
| | - Paul James
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stig Bojesen
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Mattson
- Department of Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Centre, Tel Aviv, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Centre, Tel Aviv, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Ines Zanna
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Antoinette Hollestelle
- Department of Medical Oncology, Familial Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Familial Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Mateja Krajc
- Institute of Oncology Ljubljana, Cancer Genetics Clinic, Epidemiology and Cancer Registry, Ljubljana, Slovenia
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Galego de Saúde (SERGAS), Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Oncology and Genetics Unit, Vigo, Spain
| | - Jose Esteban Castelao
- Genetic Oncology Unit, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Hakan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | | | - Vasilios Georgoulias
- Department of Medical Oncology, University General Hospital of Heraklion, Heraklion, Greece
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - D Timothy Bishop
- Division of Immunology, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, CA, USA
| | | | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Nick Orr
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
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Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv 2021; 7:eabf8711. [PMID: 33853786 PMCID: PMC8046379 DOI: 10.1126/sciadv.abf8711] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/24/2021] [Indexed: 05/19/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate-ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Luan Carvalho Martins
- Biochemistry Department, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Dominique H Smith
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tristan W Owens
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ishan Deshpande
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Gregory E Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Aye C Thwin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Justin T Biel
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jessica K Peters
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michelle Moritz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadia Herrera
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Huong T Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - James M Bennett
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
| | - Jose Brandao Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
| | - Matteo P Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Martin R Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Tyler J Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Tobias Krojer
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - George Meigs
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ailsa J Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | | | - Victor L Rangel
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, São Paulo, Brazil
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Rachael E Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexei S Soares
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jennifer L Wierman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Natalia Jura
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, San Francisco, CA 94158, USA
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Sjöström M, Zhao S, Small EJ, Ning Y, Maurice-Dror C, Foye A, Hua JJT, Li H, Beer TM, Evans CP, Rettig M, Chi KN, Alumkal JJ, Aggarwal RR, Ashworth A, Levy S, He HH, Wyatt AW, Quigley DA, Feng FY. 5-hydroxymethylcytosine as a liquid biopsy biomarker in mCRPC. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.6_suppl.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
148 Background: 5-hydroxymethylcytosine (5hmC) is an epigenetic modification which regulates gene expression and is associated with active transcription. The optimization of 5hmC sequencing in cell-free DNA (cfDNA) could therefore enable assessment of gene activity through a liquid biopsy. We aimed to investigate the 5hmC landscape of metastatic castration-resistant prostate cancer (mCRPC) and to evaluate the potential of 5hmC modifications in cfDNA as biomarkers of outcome in mCRPC patients. Methods: Genome-wide 5hmC modifications were analyzed with a low-input whole-genome 5hmC sequencing method based on selective chemical labeling in DNA from 93 mCRPC tissue biopsies previously profiled with whole-genome sequencing (WGS), RNA-sequencing and whole-genome bisulfite sequencing (WGBS). In addition, we analyzed 64 cell-free DNA (cfDNA) samples, from men with mCRPC before first-line abiraterone or enzalutamide, with both 5hmC sequencing and a conventional targeted ctDNA panel assessing common genomic alterations. Results: In mCRPC tissue samples, 5hmC enrichment was more strongly associated with gene expression than promoter methylation or copy number. Among cancer hallmark pathways, the androgen response genes had the strongest association between 5hmC and gene expression, suggesting a disease specific marking of gene activation. 5hmC patterns in cfDNA could be used to estimate the circulating tumor DNA fraction (ct-fraction), which was prognostic for overall survival (tertiles of ct-fraction, HR = 1.6 95%CI 1.1-2.3, p = 0.007). Further, 5hmC levels were indicative of gain of oncogene activity (such as AR, MYC, and PIK3CA) and loss of tumor suppressor gene activity (such as RB1, TP53 and BRCA2). The number of alterations, by 5hmC levels, of common drivers of mCRPC was prognostic for overall survival, also after adjusting for ct-fraction (adjusted p = 0.00001), and the prognostic value of common alterations detected by 5hmC sequencing versus conventional targeted ctDNA sequencing was similar. Finally, 5hmC levels in cfDNA of genes not significantly altered by copy number gain or loss (and thus not routinely included in targeted ctDNA sequencing assays), such as TOP2A and EZH2, identified a high-risk subgroup of mCRPC, which was highly prognostic for overall survival independent of ct-fraction (adjusted HR = 1.8 95%CI 1.2-2.8, p = 0.007). Conclusions: 5hmC in mCRPC tissue demonstrated an association with gene expression that was highest for prostate cancer driver genes, highlighting the ability to track disease-specific biology. 5hmC in cfDNA from men with mCRPC can be used to estimate the ct-fraction of the sample, infer activity gain and loss of common drivers of mCRPC, and identify high-risk groups of mCRPC based on alterations not commonly detected with conventional ctDNA sequencing, showing its potential as a liquid biomarker. Further studies are aimed at optimizing and validating 5hmC-based biomarkers in larger cohorts.
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Affiliation(s)
- Martin Sjöström
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Shuang Zhao
- University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Eric Jay Small
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | | | - Adam Foye
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Jun Jie T. Hua
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Haolong Li
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Tomasz M. Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | | | - Matthew Rettig
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, and VA Greater Los Angeles Healthcare System, Los Angeles, CA
| | - Kim N. Chi
- University of British Columbia, BC Cancer-Vancouver Center, Vancouver, BC, Canada
| | | | - Rahul Raj Aggarwal
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Alan Ashworth
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Housheng H. He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David A. Quigley
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Felix Y Feng
- University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
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40
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Dreyer SB, Upstill-Goddard R, Paulus-Hock V, Paris C, Lampraki EM, Dray E, Serrels B, Caligiuri G, Rebus S, Plenker D, Galluzzo Z, Brunton H, Cunningham R, Tesson M, Nourse C, Bailey UM, Jones M, Moran-Jones K, Wright DW, Duthie F, Oien K, Evers L, McKay CJ, McGregor GA, Gulati A, Brough R, Bajrami I, Pettitt S, Dziubinski ML, Candido J, Balkwill F, Barry ST, Grützmann R, Rahib L, Johns A, Pajic M, Froeling FEM, Beer P, Musgrove EA, Petersen GM, Ashworth A, Frame MC, Crawford HC, Simeone DM, Lord C, Mukhopadhyay D, Pilarsky C, Tuveson DA, Cooke SL, Jamieson NB, Morton JP, Sansom OJ, Bailey PJ, Biankin AV, Chang DK. Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer. Gastroenterology 2021; 160:362-377.e13. [PMID: 33039466 PMCID: PMC8167930 DOI: 10.1053/j.gastro.2020.09.043] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Continuing recalcitrance to therapy cements pancreatic cancer (PC) as the most lethal malignancy, which is set to become the second leading cause of cancer death in our society. The study aim was to investigate the association between DNA damage response (DDR), replication stress, and novel therapeutic response in PC to develop a biomarker-driven therapeutic strategy targeting DDR and replication stress in PC. METHODS We interrogated the transcriptome, genome, proteome, and functional characteristics of 61 novel PC patient-derived cell lines to define novel therapeutic strategies targeting DDR and replication stress. Validation was done in patient-derived xenografts and human PC organoids. RESULTS Patient-derived cell lines faithfully recapitulate the epithelial component of pancreatic tumors, including previously described molecular subtypes. Biomarkers of DDR deficiency, including a novel signature of homologous recombination deficiency, cosegregates with response to platinum (P < .001) and PARP inhibitor therapy (P < .001) in vitro and in vivo. We generated a novel signature of replication stress that predicts response to ATR (P < .018) and WEE1 inhibitor (P < .029) treatment in both cell lines and human PC organoids. Replication stress was enriched in the squamous subtype of PC (P < .001) but was not associated with DDR deficiency. CONCLUSIONS Replication stress and DDR deficiency are independent of each other, creating opportunities for therapy in DDR-proficient PC and after platinum therapy.
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Affiliation(s)
- Stephan B Dreyer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Rosie Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - Clara Paris
- Department of Pharmacological Faculty, Université Grenoble Alpes, Saint-Martin-d'Heres, France
| | - Eirini-Maria Lampraki
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bryan Serrels
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Giuseppina Caligiuri
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Selma Rebus
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Zachary Galluzzo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Holly Brunton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Richard Cunningham
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Mathias Tesson
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Craig Nourse
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Ulla-Maja Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Marc Jones
- Stratified Medicine Scotland, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Kim Moran-Jones
- College of Medicine, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Derek W Wright
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Karin Oien
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom; Greater Glasgow and Clyde Bio-repository, Pathology Department, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Lisa Evers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Colin J McKay
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | | | - Aditi Gulati
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Rachel Brough
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Ilirjana Bajrami
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Stephan Pettitt
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Michele L Dziubinski
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Juliana Candido
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Frances Balkwill
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Simon T Barry
- Bioscience, Oncology, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Robert Grützmann
- Department of Surgery, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Lola Rahib
- Pancreatic Cancer Action Network, Manhattan Beach, California
| | - Amber Johns
- The Kinghorn Cancer Centre, Darlinghurst and Garvan Institute of Medical Research, Sydney, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, Darlinghurst and Garvan Institute of Medical Research, Sydney, Australia
| | - Fieke E M Froeling
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York; Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Phillip Beer
- Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Elizabeth A Musgrove
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - Alan Ashworth
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom; University of California-San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Margaret C Frame
- Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Howard C Crawford
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Diane M Simeone
- Pancreatic Cancer Center, Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | - Chris Lord
- Cancer Research UK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, Florida
| | | | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Susanna L Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Jennifer P Morton
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Owen J Sansom
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Peter J Bailey
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia.
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom; South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia.
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Fontaine SD, Ashley GW, Houghton PJ, Kurmasheva RT, Diolaiti M, Ashworth A, Peer CJ, Nguyen R, Figg WD, Beckford-Vera DR, Santi DV. A Very Long-Acting PARP Inhibitor Suppresses Cancer Cell Growth in DNA Repair-Deficient Tumor Models. Cancer Res 2020; 81:1076-1086. [PMID: 33323380 DOI: 10.1158/0008-5472.can-20-1741] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/21/2020] [Accepted: 12/10/2020] [Indexed: 11/16/2022]
Abstract
PARP inhibitors are approved for treatment of cancers with BRCA1 or BRCA2 defects. In this study, we prepared and characterized a very long-acting PARP inhibitor. Synthesis of a macromolecular prodrug of talazoparib (TLZ) was achieved by covalent conjugation to a PEG40kDa carrier via a β-eliminative releasable linker. A single injection of the PEG∼TLZ conjugate was as effective as ∼30 daily oral doses of TLZ in growth suppression of homologous recombination-defective tumors in mouse xenografts. These included the KT-10 Wilms' tumor with a PALB2 mutation, the BRCA1-deficient MX-1 triple-negative breast cancer, and the BRCA2-deficient DLD-1 colon cancer; the prodrug did not inhibit an isogenic DLD-1 tumor with wild-type BRCA2. Although the half-life of PEG∼TLZ and released TLZ in the mouse was only ∼1 day, the exposure of released TLZ from a single safe, effective dose of the prodrug exceeded that of oral TLZ given daily over one month. μPET/CT imaging showed high uptake and prolonged retention of an 89Zr-labeled surrogate of PEG∼TLZ in the MX-1 BRCA1-deficient tumor. These data suggest that the long-lasting antitumor effect of the prodrug is due to a combination of its long t 1/2, the high exposure of TLZ released from the prodrug, increased tumor sensitivity upon continued exposure, and tumor accumulation. Using pharmacokinetic parameters of TLZ in humans, we designed a long-acting PEG∼TLZ for humans that may be superior in efficacy to daily oral TLZ and would be useful for treatment of PARP inhibitor-sensitive cancers in which oral medications are not tolerated. SIGNIFICANCE: These findings demonstrate that a single injection of a long-acting prodrug of the PARP inhibitor talazoparib in murine xenografts provides tumor suppression equivalent to a month of daily dosing of talazoparib.
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Affiliation(s)
| | | | - Peter J Houghton
- Greehey Children's Cancer Research Institute, UT Health San Antonio, Texas
| | | | - Morgan Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Cody J Peer
- Pharmacology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ryan Nguyen
- Pharmacology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - William D Figg
- Pharmacology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Denis R Beckford-Vera
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
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Chen WS, Haynes WA, Waitz R, Kamath K, Vega-Crespo A, Shrestha R, Zhang M, Foye A, Baselga Carretero I, Perez Garcilazo I, Zhang M, Zhao SG, Sjöström M, Quigley DA, Chou J, Beer TM, Rettig M, Gleave M, Evans CP, Lara P, Chi KN, Reiter RE, Alumkal JJ, Ashworth A, Aggarwal R, Small EJ, Daugherty PS, Ribas A, Oh DY, Shon JC, Feng FY. Autoantibody Landscape in Patients with Advanced Prostate Cancer. Clin Cancer Res 2020; 26:6204-6214. [PMID: 32967941 PMCID: PMC7710628 DOI: 10.1158/1078-0432.ccr-20-1966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/03/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE Autoantibody responses in cancer are of great interest, as they may be concordant with T-cell responses to cancer antigens or predictive of response to cancer immunotherapies. Thus, we sought to characterize the antibody landscape of metastatic castration-resistant prostate cancer (mCRPC). EXPERIMENTAL DESIGN Serum antibody epitope repertoire analysis (SERA) was performed on patient serum to identify tumor-specific neoepitopes. Somatic mutation-specific neoepitopes were investigated by associating serum epitope enrichment scores with whole-genome sequencing results from paired solid tumor metastasis biopsies and germline blood samples. A protein-based immunome-wide association study (PIWAS) was performed to identify significantly enriched epitopes, and candidate serum antibodies enriched in select patients were validated by ELISA profiling. A distinct cohort of patients with melanoma was evaluated to validate the top cancer-specific epitopes. RESULTS SERA was performed on 1,229 serum samples obtained from 72 men with mCRPC and 1,157 healthy control patients. Twenty-nine of 6,636 somatic mutations (0.44%) were associated with an antibody response specific to the mutated peptide. PIWAS analyses identified motifs in 11 proteins, including NY-ESO-1 and HERVK-113, as immunogenic in mCRPC, and ELISA confirmed serum antibody enrichment in candidate patients. Confirmatory PIWAS, Identifying Motifs Using Next-generation sequencing Experiments (IMUNE), and ELISA analyses performed on serum samples from 106 patients with melanoma similarly revealed enriched cancer-specific antibody responses to NY-ESO-1. CONCLUSIONS We present the first large-scale profiling of autoantibodies in advanced prostate cancer, utilizing a new antibody profiling approach to reveal novel cancer-specific antigens and epitopes. Our study recovers antigens of known importance and identifies novel tumor-specific epitopes of translational interest.
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Affiliation(s)
- William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | | | | | - Agustin Vega-Crespo
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Ivan Perez Garcilazo
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Shuang G Zhao
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Matthew Rettig
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Martin Gleave
- University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Primo Lara
- University of California Davis, Davis, California
| | - Kim N Chi
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Department of Urology, University of California Los Angeles, Los Angeles, California
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Antoni Ribas
- Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, California
| | - David Y Oh
- Department of Medicine, University of California San Francisco, San Francisco, California
| | | | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
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Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, Aimon A, Bennett JM, Neto JB, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs M, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv 2020:2020.11.24.393405. [PMID: 33269349 PMCID: PMC7709169 DOI: 10.1101/2020.11.24.393405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, CA, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, CA, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, CA, USA
| | - Iris D. Young
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Luan Carvalho Martins
- Biochemistry Department, Institute for Biological Sciences, Federal University of Minas Gerais. Belo Horizonte, Brazil
| | - Dominique H. Smith
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA, USA
| | - Ursula Schulze-Gahmen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Tristan W. Owens
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Ishan Deshpande
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Gregory E. Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Aye C. Thwin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Justin T. Biel
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Jessica K. Peters
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Michelle Moritz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Nadia Herrera
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Huong T. Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - QCRG Structural Biology Consortium
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James M. Bennett
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
| | - Jose Brandao Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Tyler J. Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Tobias Krojer
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - George Meigs
- Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ailsa J. Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | | | - Victor L Rangel
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, São Paulo, Brazil
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Rachael E. Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | | | - Jennifer L. Wierman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Natalia Jura
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA, USA
| | - John Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA, USA
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
- Institute for Neurodegenerative Disease, University of California San Francisco, CA, USA
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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44
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Guler GD, Ning Y, Ku CJ, Phillips T, McCarthy E, Ellison CK, Bergamaschi A, Collin F, Lloyd P, Scott A, Antoine M, Wang W, Chau K, Ashworth A, Quake SR, Levy S. Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA. Nat Commun 2020; 11:5270. [PMID: 33077732 PMCID: PMC7572413 DOI: 10.1038/s41467-020-18965-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 09/18/2020] [Indexed: 12/15/2022] Open
Abstract
Pancreatic cancer is often detected late, when curative therapies are no longer possible. Here, we present non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by 5-hydroxymethylcytosine (5hmC) changes in circulating cell free DNA from a PDAC cohort (n = 64) in comparison with a non-cancer cohort (n = 243). Differential hydroxymethylation is found in thousands of genes, most significantly in genes related to pancreas development or function (GATA4, GATA6, PROX1, ONECUT1, MEIS2), and cancer pathogenesis (YAP1, TEAD1, PROX1, IGF1). cfDNA hydroxymethylome in PDAC cohort is differentially enriched for genes that are commonly de-regulated in PDAC tumors upon activation of KRAS and inactivation of TP53. Regularized regression models built using 5hmC densities in genes perform with AUC of 0.92 (discovery dataset, n = 79) and 0.92-0.94 (two independent test sets, n = 228). Furthermore, tissue-derived 5hmC features can be used to classify PDAC cfDNA (AUC = 0.88). These findings suggest that 5hmC changes enable classification of PDAC even during early stage disease.
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Affiliation(s)
- Gulfem D Guler
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Yuhong Ning
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Chin-Jen Ku
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Tierney Phillips
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Erin McCarthy
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | | | - Anna Bergamaschi
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Francois Collin
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Paul Lloyd
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Aaron Scott
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Michael Antoine
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Wendy Wang
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA
| | - Kim Chau
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA, 94304, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Samuel Levy
- Bluestar Genomics, 185 Berry Street, Lobby 4, Suite 210, San Francisco, CA, 94107, USA.
- Bluestar Genomics, 10578 Science Center Drive Suite 210, San Diego, CA, 92121, USA.
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45
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Bergamaschi A, Ku J, Ning Y, Collin F, Ellison C, Phillips T, McCarthy E, Wang W, Antoine M, Haan D, Scott A, Lloyd P, Guler G, Ashworth A, Quake S, Levy S. Abstract 783: Epigenomic detection of multiple cancers in plasma derived cell free DNA. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Our feasibility study employed a novel genomic detection methodology that enriches 5-hydroxymethylcytosine (5hmC) loci in cell free DNA (cfDNA) from the plasma of cancer patients using click chemistry coupled with sequencing and machine learning based classification methods. These classification methods were developed to detect the presence of disease in the plasma of cancer and control subjects. Cancer and control patient cfDNA cohorts were accrued from multiple sites consisting of 48 breast, 55 lung, 32 prostate and 2 pancreatic datasets consisting of 41 and 53 cancer subjects (Set 1 and 2). In addition, a control cohort of 260 subjects (non-cancer) was employed to match cancer patient demographics (age, sex and smoking status) in a case-control study design.
Methods: Machine learning methods, applied to each cancer case cohort individually, with a balancing non-cancer cohort, were able to classify cancer and control samples. Measures of predictive performance using 5-fold cross validation coupled with out-of-fold Area Under the Receiver Operating Characteristic Curve (AUROC) measures were employed. Gene sets selected as part of biomarker discovery were further analyzed for disease relevance using pathway analysis tools (GSEA, mSigDB).
Results: 260 controls and 229 cancers from four disease types (breast, lung, pancreas and prostate) were analyzed; more than 60% of cancer patients had early stage disease (I or II). Predictive performance, employing AUROC measures, was established for breast (0.89), lung (0.84), pancreas (set 1 - 0.95 and 2 - 0.93) and prostate (0.83). The genes defining each of these predictive models were enriched for pathways relevant to disease specific etiology, notably in the control of gene regulation in these same pathways. The breast cancer cohort consisted primarily of stage I and II patients including tumors < 2 cm and these samples exhibited a higher prediction probability score. The prostate cancer cohort consisted of both indolent and aggressive disease sample and prediction performance was equally high for both (AUROC for indolent vs aggressive was 0.81 and 0.77, respectively).
Conclusions: These findings suggest that 5hmC changes in cfDNA enable non-invasive detection of early stage breast, pancreatic, prostate, and lung cancers. Furthermore, 5hmC profiling in cfDNA may enable the prediction of clinically relevant features such as tumor size in breast adenocarcinoma or indolent disease in prostate cancer. Finally, this study identified a suite of 5hmC biomarkers that may be further validated in larger, and more diverse, patient cohorts.
Citation Format: Anna Bergamaschi, Jeremy Ku, Yuhong Ning, Francois Collin, Chris Ellison, Tierney Phillips, Erin McCarthy, Wendy Wang, Michael Antoine, David Haan, Aaron Scott, Paul Lloyd, Gulfem Guler, Alan Ashworth, Stephen Quake, Samuel Levy. Epigenomic detection of multiple cancers in plasma derived cell free DNA [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 783.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Alan Ashworth
- 2UCSF Helen Diller Family Comprehensive Cancer Cent, San Francisco, CA
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46
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Fontaine SD, Ashley GW, Houghton PJ, Kurmasheva R, Diolati M, Ashworth A, Santi DV. Abstract LB-060: A very long-acting poly(ADP-ribose) polymerase inhibitor. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: The purpose of this work was to prepare and characterize the anti-tumor properties of a prodrug for a very long-acting of poly(ADP-ribose) polymerase (PARP) inhibitor. Background: Four PARP inhibitors (PARPi) have been approved for QD oral use in treatment of human cancers. It is believed that PARP requires continuous inhibition for optimal anti-tumor effects, but, as with any drug with a short t1/2, daily administered PARPi exhibit high Cmax values and peak-to-trough excursions. We speculated that the prolonged exposure and lower Cmax and Cmax/Cmin of a long-acting PARPi might provide a more effective, less toxic therapeutic. In choosing which PARPi to target, a major consideration was whether the carrier has capacity to deliver sufficient levels of the drug over a long dosing interval. Talazoparib (TLZ) was chosen for this study because it is the most potent of the PARP inhibitors, requiring only 1 mg/day in adults compared to hundreds of mg/day for other PARPi's. Experimental procedures: We prepared a long-acting prodrug of TLZ by attaching it to a PEG40kDa carrier by a β-eliminative releasable linker. The chemistry was achieved by a novel alkylation of TLZ at the poorly acidic 2-NH of the phthalazinone moiety with an O-azidoalkyl-N-alkyl-N-chloromethyl carbamate, followed by coupling to PEG-cyclooctyne. Daily PO doses of TLZ or a single IP injection of the PEG-TLZ conjugate were administered to xenografts in mice possessing defects in homologous recombination - either a PALB2 mutation in the KT-10 Wilms tumor, or a BRCA1-deficient MX-1 triple-negative breast cancer. New data: PEG~TLZ was highly effective in treating both KT-10 and MX-1 xenografts. Although the t1/2 of TLZ in the mouse is only ~3 hr, tumor growth in animals treated with PEG~TLZ was suppressed for about one month. The EFS T/C values - the ratio of the median time to event between treated and control groups - of single injections of ~5 mg TLZ/kg as PEG~TLZ in either tumor was more than 4, indicating the drug is a highly active agent at low doses. The amount of TLZ in a single efficacious dose of the PEG~TLZ conjugate was equivalent to the same amount of free TLZ administered in divided daily doses for 4 or more weeks. Although we did not investigate scheduling, dosing PEG~TLZ once every 3 to 4 weeks should be sufficient to suppress tumor growth for extended periods. Conclusion: We developed a novel method of conjugating linkers to the 2N of the phthalazinone moiety of PARPi. We prepared a cleavable PEG~TLZ that releases TLZ with a t1/2 of 160 hr at pH 7.4. In mouse xenografts of tumors with defective HR, single non-toxic doses of PEG~TLZ suppresses tumor growth for ~1 month, and are equi-effective to QD administration of TLZ over that period. We posit that the long lasting effect is due to the long t1/2 of the prodrug, increased sensitivity of the tumor upon continued exposure to TLZ, tumor accumulation of the 15 nm nanomolecule, and counteracting drug resistance by efflux pumps.
Citation Format: Shaun D. Fontaine, Gary W. Ashley, Peter J. Houghton, Raushan Kurmasheva, Morgan Diolati, Alan Ashworth, Daniel V. Santi. A very long-acting poly(ADP-ribose) polymerase inhibitor [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-060.
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Affiliation(s)
| | | | | | | | - Morgan Diolati
- 3UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Alan Ashworth
- 3UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
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47
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Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet 2020; 52:778-789. [PMID: 32661416 PMCID: PMC7454228 DOI: 10.1038/s41588-020-0648-8] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes only detectable with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hyper-methylation and somatic mutations in TET2, DNMT3B, IDH1, and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer and provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Denise Playdle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Travis J Barnard
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adina M Bailey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ruhollah Moussavi-Baygi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - S Laura Chang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Division of Hematology/Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA.,Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Yvonne Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Nupam P Mahajan
- Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Surgery, Washington University, St. Louis, MO, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.,Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.,Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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48
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020; 583:459-468. [PMID: 32353859 PMCID: PMC7431030 DOI: 10.1038/s41586-020-2286-9] [Citation(s) in RCA: 2828] [Impact Index Per Article: 707.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Sachdeva A, Gouge J, Kontovounisios C, Nikolaou S, Ashworth A, Lim K, Chong I. Klotho and the Treatment of Human Malignancies. Cancers (Basel) 2020; 12:cancers12061665. [PMID: 32585905 PMCID: PMC7352559 DOI: 10.3390/cancers12061665] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
Klotho was first discovered as an anti-ageing protein linked to a number of age-related disease processes, including cardiovascular, renal, musculoskeletal, and neurodegenerative conditions. Emerging research has also demonstrated a potential therapeutic role for Klotho in cancer biology, which is perhaps unsurprising given that cancer and ageing share similar molecular hallmarks. In addition to functioning as a tumour suppressor in numerous solid tumours and haematological malignancies, Klotho represents a candidate therapeutic target for patients with these diseases, the majority of whom have limited treatment options. Here, we examine contemporary evidence evaluating the anti-neoplastic effects of Klotho and describe the modulation of downstream oncogenic signalling pathways, including Wnt/β-catenin, FGF, IGF1, PIK3K/AKT, TGFβ, and the Unfolded Protein Response. We also discuss possible approaches to developing therapeutic Klotho and consider technological advances that may facilitate the delivery of Klotho through gene therapy.
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Affiliation(s)
- Aishani Sachdeva
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Jerome Gouge
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK;
| | - Christos Kontovounisios
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Stella Nikolaou
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA;
| | - Kenneth Lim
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202-5181, USA;
| | - Irene Chong
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- The Institute of Cancer Research, London SW3 6JB, UK
- Correspondence:
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Bergamaschi A, Haan D, Ku J, Ning Y, Ellison C, Guler G, Phillips T, McCarthy E, Antoine M, Nguyen A, Scott A, Lloyd P, Ashworth A, Bethel K, Levy S. Effect of detection of epigenomic changes in plasma-derived cell-free DNA on multicancer classification. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1539 Background: Epigenomic changes in DNA methylation patterns are more precisely delineated by active demethylation events as marked by 5-hydroxymethylation (5hmC) of cytosine residues. 5hmC appears to be dynamically modulated in tumor tissues and can be employed as a cancer biomarker. Strategies which interrogate 5hmC genome-wide patterns in a liquid biopsy context may provide efficient and precise technology for early cancer screening and detection. In this study we identified genome-wide 5hmC changes in plasma based circulating free DNA (cfDNA) from breast, colorectal, lung, pancreatic and prostate cancer patients versus non-cancer individuals. Methods: cfDNA was isolated from plasma, enriched for the 5hmC fraction using novel click-chemistry protocol for labelling followed by sequencing and alignment to a reference genome to construct features sets of 5hmC patterns. Regularized classification models were constructed to classify cancer samples apart from non-cancer. Results: > 500 non-cancer individuals and > 500 cancer patients across five cancer types (breast, colorectal, lung, pancreas and prostate) were included in this study. About 60% of the cancer samples were early stage disease (I or II). The ability to classify non-cancer versus cancer patients was evaluated by 5-fold cross validation of our trained prediction models. Our models were able to classify all breast cancer with a test auROC of 0.86 while prediction model classification for ER negative samples had an auROC of 0.92. Colorectal performance auROC was 0.9; lung auROC = 0.92, pancreatic auROC = 0.97 and prostate auROC = 0.91. Overall sensitivity range, when allowing 2% false positive, was between 85% and 52%. Further using 5hmC signal in blood we were able to identify several signaling pathways specifically relevant to the biology of the cancers investigated. Conclusions: These findings further demonstrate that 5hmC changes in cfDNA enable non-invasive detection of breast, colorectal, lung pancreatic, and prostate cancers. Further, 5hmC signals enabled the identification of a suite of cancer signaling pathways differentially enriched in cancers versus non-cancers. These data suggest that dynamic changes in tumor cell methylation, detectable through 5-hydroxymethylation, are contained in the circulating blood and signal active disease biology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
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