1
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Burghi V, Paradis JS, Officer A, Adame-Garcia SR, Wu X, Matthees ESF, Barsi-Rhyne B, Ramms DJ, Clubb L, Acosta M, Tamayo P, Bouvier M, Inoue A, von Zastrow M, Hoffmann C, Gutkind JS. Gαs is dispensable for β-arrestin coupling but dictates GRK selectivity and is predominant for gene expression regulation by β2-adrenergic receptor. J Biol Chem 2023; 299:105293. [PMID: 37774973 PMCID: PMC10641165 DOI: 10.1016/j.jbc.2023.105293] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/03/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023] Open
Abstract
β-arrestins play a key role in G protein-coupled receptor (GPCR) internalization, trafficking, and signaling. Whether β-arrestins act independently of G protein-mediated signaling has not been fully elucidated. Studies using genome-editing approaches revealed that whereas G proteins are essential for mitogen-activated protein kinase activation by GPCRs., β-arrestins play a more prominent role in signal compartmentalization. However, in the absence of G proteins, GPCRs may not activate β-arrestins, thereby limiting the ability to distinguish G protein from β-arrestin-mediated signaling events. We used β2-adrenergic receptor (β2AR) and its β2AR-C tail mutant expressed in human embryonic kidney 293 cells wildtype or CRISPR-Cas9 gene edited for Gαs, β-arrestin1/2, or GPCR kinases 2/3/5/6 in combination with arrestin conformational sensors to elucidate the interplay between Gαs and β-arrestins in controlling gene expression. We found that Gαs is not required for β2AR and β-arrestin conformational changes, β-arrestin recruitment, and receptor internalization, but that Gαs dictates the GPCR kinase isoforms involved in β-arrestin recruitment. By RNA-Seq analysis, we found that protein kinase A and mitogen-activated protein kinase gene signatures were activated by stimulation of β2AR in wildtype and β-arrestin1/2-KO cells but absent in Gαs-KO cells. These results were validated by re-expressing Gαs in the corresponding KO cells and silencing β-arrestins in wildtype cells. These findings were extended to cellular systems expressing endogenous levels of β2AR. Overall, our results support that Gs is essential for β2AR-promoted protein kinase A and mitogen-activated protein kinase gene expression signatures, whereas β-arrestins initiate signaling events modulating Gαs-driven nuclear transcriptional activity.
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Affiliation(s)
- Valeria Burghi
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Justine S Paradis
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Adam Officer
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Sendi Rafael Adame-Garcia
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Xingyu Wu
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Edda S F Matthees
- Institut für Molekulare Zellbiologie, CMB - Center for Molecular Biomedicine, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Benjamin Barsi-Rhyne
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
| | - Dana J Ramms
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Lauren Clubb
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Monica Acosta
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Pablo Tamayo
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Michel Bouvier
- Department of Biochemistry and Molecular Medicine, Institute for Research in Immunology and Cancer, Université de Montréal, Québec, Canada
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Mark von Zastrow
- Department of Psychiatry and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA
| | - Carsten Hoffmann
- Institut für Molekulare Zellbiologie, CMB - Center for Molecular Biomedicine, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - J Silvio Gutkind
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA.
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2
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Ruiz-Saenz A, Atreya CE, Wang C, Pan B, Dreyer CA, Brunen D, Prahallad A, Muñoz DP, Ramms DJ, Burghi V, Spassov DS, Fewings E, Hwang YC, Cowdrey C, Moelders C, Schwarzer C, Wolf DM, Hann B, VandenBerg SR, Shokat K, Moasser MM, Bernards R, Gutkind JS, van 't Veer LJ, Coppé JP. A reversible SRC-relayed COX2 inflammatory program drives resistance to BRAF and EGFR inhibition in BRAF V600E colorectal tumors. Nat Cancer 2023; 4:240-256. [PMID: 36759733 PMCID: PMC9970872 DOI: 10.1038/s43018-022-00508-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/21/2022] [Indexed: 02/11/2023]
Abstract
BRAFV600E mutation confers a poor prognosis in metastatic colorectal cancer (CRC) despite combinatorial targeted therapies based on the latest understanding of signaling circuitry. To identify parallel resistance mechanisms induced by BRAF-MEK-EGFR co-targeting, we used a high-throughput kinase activity mapping platform. Here we show that SRC kinases are systematically activated in BRAFV600E CRC following targeted inhibition of BRAF ± EGFR and that coordinated targeting of SRC with BRAF ± EGFR increases treatment efficacy in vitro and in vivo. SRC drives resistance to BRAF ± EGFR targeted therapy independently of ERK signaling by inducing transcriptional reprogramming through β-catenin (CTNNB1). The EGFR-independent compensatory activation of SRC kinases is mediated by an autocrine prostaglandin E2 loop that can be blocked with cyclooxygenase-2 (COX2) inhibitors. Co-targeting of COX2 with BRAF + EGFR promotes durable suppression of tumor growth in patient-derived tumor xenograft models. COX2 inhibition represents a drug-repurposing strategy to overcome therapeutic resistance in BRAFV600E CRC.
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Affiliation(s)
- Ana Ruiz-Saenz
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Departments of Cell Biology & Medical Oncology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Chloe E Atreya
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Changjun Wang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bo Pan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Courtney A Dreyer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Diede Brunen
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anirudh Prahallad
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Denise P Muñoz
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Dana J Ramms
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Valeria Burghi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Danislav S Spassov
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
| | - Eleanor Fewings
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Institute for Computational Biomedicine, Heidelberg, Germany
| | - Yeonjoo C Hwang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Cynthia Cowdrey
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Christina Moelders
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Cecilia Schwarzer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Denise M Wolf
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Scott R VandenBerg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Kevan Shokat
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mark M Moasser
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - René Bernards
- Division of Molecular Carcinogenesis and Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J Silvio Gutkind
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Laura J van 't Veer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jean-Philippe Coppé
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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3
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Gilardi M, Saddawi-Konefka R, Wu VH, Lopez-Ramirez MA, Wang Z, Soto F, Ramms DJ, Proietto M, Mikulski Z, Miki H, Sharabi A, Kupor D, Rueda R, Hollern DP, Wang J, Gutkind JS. Microneedle-mediated Intratumoral Delivery of Anti-CTLA-4 Promotes cDC1-dependent Eradication of Oral Squamous Cell Carcinoma with Limited irAEs. Mol Cancer Ther 2022; 21:616-624. [PMID: 35086958 PMCID: PMC8983493 DOI: 10.1158/1535-7163.mct-21-0234] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 03/12/2021] [Revised: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 11/16/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) ranks sixth in cancer incidence worldwide and has a 5-year survival rate of only 63%. Immunotherapies-principally immune checkpoint inhibitors (ICI), such as anti-PD-1 and anti-CTLA-4 antibodies that restore endogenous antitumor T-cell immunity-offer the greatest promise for HNSCC treatment. Anti-PD-1 has been recently approved for first-line treatment of recurrent and metastatic HNSCC; however, less than 20% of patients show clinical benefit and durable responses. In addition, the clinical application of ICI has been limited by immune-related adverse events (irAE) consequent to compromised peripheral immune tolerance. Although irAEs are often reversible, they can become severe, prompting premature therapy termination or becoming life threatening. To address the irAEs inherent to systemic ICI therapy, we developed a novel, local delivery strategy based upon an array of soluble microneedles (MN). Using our recently reported syngeneic, tobacco-signature murine HNSCC model, we found that both systemic and local-MN anti-CTLA-4 therapy lead to >90% tumor response, which is dependent on CD8 T cells and conventional dendritic cell type 1 (cDC1). However, local-MN delivery limited the distribution of anti-CTLA-4 antibody from areas distal to draining lymphatic basins. Employing Foxp3-GFPDTR transgenic mice to interrogate irAEs in vivo, we found that local-MN delivery of anti-CTLA-4 protects animals from irAEs observed with systemic therapy. Taken together, our findings support the exploration of MN-intratumoral ICI delivery as a viable strategy for HNSCC treatment with reduced irAEs, and the opportunity to target cDC1s as part of multimodal treatment options to boost ICI therapy.
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Affiliation(s)
- Mara Gilardi
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
- Salk cancer center, La Jolla, CA, 92037, USA
- Nomis cancer center for immunology and microbial pathogenesis, La Jolla, CA, 92037, USA
| | - Robert Saddawi-Konefka
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H. Wu
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Zhiyong Wang
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Fernando Soto
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dana J. Ramms
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Marco Proietto
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zbigniew Mikulski
- Microscopy Core Facility, La Jolla Institute for Immunology, La Jolla, CA, 92093, USA
| | - Haruka Miki
- Center of Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA, 92093, USA
| | - Andrew Sharabi
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel Kupor
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ricardo Rueda
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel P. Hollern
- Salk cancer center, La Jolla, CA, 92037, USA
- Nomis cancer center for immunology and microbial pathogenesis, La Jolla, CA, 92037, USA
| | - Joseph Wang
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - J. Silvio Gutkind
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
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4
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Ramms DJ, Raimondi F, Arang N, Herberg FW, Taylor SS, Gutkind JS. G αs-Protein Kinase A (PKA) Pathway Signalopathies: The Emerging Genetic Landscape and Therapeutic Potential of Human Diseases Driven by Aberrant G αs-PKA Signaling. Pharmacol Rev 2021; 73:155-197. [PMID: 34663687 DOI: 10.1124/pharmrev.120.000269] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many of the fundamental concepts of signal transduction and kinase activity are attributed to the discovery and crystallization of cAMP-dependent protein kinase, or protein kinase A. PKA is one of the best-studied kinases in human biology, with emphasis in biochemistry and biophysics, all the way to metabolism, hormone action, and gene expression regulation. It is surprising, however, that our understanding of PKA's role in disease is largely underappreciated. Although genetic mutations in the PKA holoenzyme are known to cause diseases such as Carney complex, Cushing syndrome, and acrodysostosis, the story largely stops there. With the recent explosion of genomic medicine, we can finally appreciate the broader role of the Gαs-PKA pathway in disease, with contributions from aberrant functioning G proteins and G protein-coupled receptors, as well as multiple alterations in other pathway components and negative regulators. Together, these represent a broad family of diseases we term the Gαs-PKA pathway signalopathies. The Gαs-PKA pathway signalopathies encompass diseases caused by germline, postzygotic, and somatic mutations in the Gαs-PKA pathway, with largely endocrine and neoplastic phenotypes. Here, we present a signaling-centric review of Gαs-PKA-driven pathophysiology and integrate computational and structural analysis to identify mutational themes commonly exploited by the Gαs-PKA pathway signalopathies. Major mutational themes include hotspot activating mutations in Gαs, encoded by GNAS, and mutations that destabilize the PKA holoenzyme. With this review, we hope to incite further study and ultimately the development of new therapeutic strategies in the treatment of a wide range of human diseases. SIGNIFICANCE STATEMENT: Little recognition is given to the causative role of Gαs-PKA pathway dysregulation in disease, with effects ranging from infectious disease, endocrine syndromes, and many cancers, yet these disparate diseases can all be understood by common genetic themes and biochemical signaling connections. By highlighting these common pathogenic mechanisms and bridging multiple disciplines, important progress can be made toward therapeutic advances in treating Gαs-PKA pathway-driven disease.
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Affiliation(s)
- Dana J Ramms
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Francesco Raimondi
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Nadia Arang
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Friedrich W Herberg
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Susan S Taylor
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - J Silvio Gutkind
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
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5
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Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O'Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T, Krogan NJ. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science 2021; 374:eabf2911. [PMID: 34591642 DOI: 10.1126/science.abf2911] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Danielle L Swaney
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Dana J Ramms
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Department of Pharmacology, University of California San Diego, La Jolla, CA.,Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Zhiyong Wang
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Jisoo Park
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Yusuke Goto
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Margaret Soucheray
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Neil Bhola
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Kyumin Kim
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Fan Zheng
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Yan Zeng
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Michael McGregor
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Kari A Herrington
- Department of Biochemistry and Biophysics Center for Advanced Light Microscopy at UCSF, University of California San Francisco, San Francisco, CA, USA
| | - Rachel O'Keefe
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Nan Jin
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Nathan K VanLandingham
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - John Von Dollen
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Mehdi Bouhaddou
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - David Jimenez-Morales
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Kirsten Obernier
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Jason F Kreisberg
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Minkyu Kim
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
| | - Daniel E Johnson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Natalia Jura
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer R Grandis
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - J Silvio Gutkind
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Department of Pharmacology, University of California San Diego, La Jolla, CA.,Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Trey Ideker
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.,Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA.,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science, University of California San Diego, La Jolla, CA, USA
| | - Nevan J Krogan
- 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.,The Cancer Cell Map Initiative, San Francisco and La Jolla, CA
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Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu S, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ, Ideker T. Interpretation of cancer mutations using a multiscale map of protein systems. Science 2021; 374:eabf3067. [PMID: 34591613 PMCID: PMC9126298 DOI: 10.1126/science.abf3067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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] [Indexed: 12/14/2022]
Abstract
A major goal of cancer research is to understand how mutations distributed across diverse genes affect common cellular systems, including multiprotein complexes and assemblies. Two challenges—how to comprehensively map such systems and how to identify which are under mutational selection—have hindered this understanding. Accordingly, we created a comprehensive map of cancer protein systems integrating both new and published multi-omic interaction data at multiple scales of analysis. We then developed a unified statistical model that pinpoints 395 specific systems under mutational selection across 13 cancer types. This map, called NeST (Nested Systems in Tumors), incorporates canonical processes and notable discoveries, including a PIK3CA-actomyosin complex that inhibits phosphatidylinositol 3-kinase signaling and recurrent mutations in collagen complexes that promote tumor proliferation. These systems can be used as clinical biomarkers and implicate a total of 548 genes in cancer evolution and progression. This work shows how disparate tumor mutations converge on protein assemblies at different scales.
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Affiliation(s)
- Fan Zheng
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Marcus R. Kelly
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Dana J. Ramms
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Marissa L. Heintschel
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kai Tao
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Beril Tutuncuoglu
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - John J. Lee
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Keiichiro Ono
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Helene Foussard
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Michael Chen
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kari A. Herrington
- Department of Biochemistry and Biophysics Center for Advanced Light Microscopy at UCSF, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Erica Silva
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sophie Liu
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jing Chen
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Christopher Churas
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Wilson
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Anton Kratz
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Rudolf T. Pillich
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Devin N. Patel
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Jisoo Park
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Brent Kuenzi
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Michael K. Yu
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Katherine Licon
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Dexter Pratt
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jason F. Kreisberg
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
| | - Minkyu Kim
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Danielle L. Swaney
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, OR, 97201, USA
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Stephanie I. Fraley
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - J. Silvio Gutkind
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Nevan J. Krogan
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA 94158, USA
- The J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, CA, USA
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