1
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Venkadakrishnan VB, Presser AG, Singh R, Booker MA, Traphagen NA, Weng K, Voss NC, Mahadevan NR, Mizuno K, Puca L, Idahor O, Ku SY, Bakht MK, Borah AA, Herbert ZT, Tolstorukov MY, Barbie DA, Rickman DS, Brown M, Beltran H. Lineage-specific canonical and non-canonical activity of EZH2 in advanced prostate cancer subtypes. Res Sq 2024:rs.3.rs-3935288. [PMID: 38405800 PMCID: PMC10889062 DOI: 10.21203/rs.3.rs-3935288/v1] [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: 02/27/2024]
Abstract
Enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase and emerging therapeutic target that is overexpressed in most castration-resistant prostate cancers and implicated as a driver of disease progression and resistance to hormonal therapies. Here we define the lineage-specific action and differential activity of EZH2 in both prostate adenocarcinoma (PRAD) and neuroendocrine prostate cancer (NEPC) subtypes of advanced prostate cancer to better understand the role of EZH2 in modulating differentiation, lineage plasticity, and to identify mediators of response and resistance to EZH2 inhibitor therapy. Mechanistically, EZH2 modulates bivalent genes that results in upregulation of NEPC-associated transcriptional drivers (e.g., ASCL1) and neuronal gene programs, and leads to forward differentiation after targeting EZH2 in NEPC. Subtype-specific downstream effects of EZH2 inhibition on cell cycle genes support the potential rationale for co-targeting cyclin/CDK to overcome resistance to EZH2 inhibition.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Loredana Puca
- Division of Medical Oncology, Weill Cornell Medicine
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2
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2024; 187:1016. [PMID: 38364782 DOI: 10.1016/j.cell.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
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3
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Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell Rep 2023; 42:113564. [PMID: 38100350 PMCID: PMC10842760 DOI: 10.1016/j.celrep.2023.113564] [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: 06/01/2023] [Revised: 10/05/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity, we defined transcriptional, epigenetic, and metabolic subtypes and subtype-driving super-enhancers and transcription factors by combining functional and molecular profiling with computational analyses. Single-cell RNA sequencing revealed relative homogeneity of the major transcriptional subtypes (luminal, basal, and mesenchymal) within samples. We found that mesenchymal TNBCs share features with mesenchymal neuroblastoma and rhabdoid tumors and that the PRRX1 transcription factor is a key driver of these tumors. PRRX1 is sufficient for inducing mesenchymal features in basal but not in luminal TNBC cells via reprogramming super-enhancer landscapes, but it is not required for mesenchymal state maintenance or for cellular viability. Our comprehensive, large-scale, multiplatform, multiomics study of both experimental and clinical TNBC is an important resource for the scientific and clinical research communities and opens venues for future investigation.
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Affiliation(s)
- Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayati Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kodie Garza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Anushree Gulvady
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Veerle W Daniels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huang Xiao-Yun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Pyrdol
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | | | - Raga Vadhi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alba Font-Tello
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert Witwicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Benedetto Diciaccio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ashim Subedee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Department of Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kai W Wucherpfennig
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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4
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Alsamraae M, Costanzo-Garvey D, Teply BA, Boyle S, Sommerville G, Herbert ZT, Morrissey C, Dafferner AJ, Abdalla MY, Fallet RW, Kielian T, Jensen-Smith H, deOliveira EI, Chen K, Bettencourt IA, Wang JM, McVicar DW, Keeley T, Yu F, Cook LM. Androgen receptor inhibition suppresses anti-tumor neutrophil response against bone metastatic prostate cancer via regulation of TβRI expression. Cancer Lett 2023; 579:216468. [PMID: 37940068 PMCID: PMC10710875 DOI: 10.1016/j.canlet.2023.216468] [Citation(s) in RCA: 1] [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: 07/14/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Bone metastatic disease of prostate cancer (PCa) is incurable and progression in bone is largely dictated by tumor-stromal interactions in the bone microenvironment. We showed previously that bone neutrophils initially inhibit bone metastatic PCa growth yet metastatic PCa becomes resistant to neutrophil response. Further, neutrophils isolated from tumor-bone lost their ability to suppress tumor growth through unknown mechanisms. With this study, our goal was to define the impact of metastatic PCa on neutrophil function throughout tumor progression and to determine the potential of neutrophils as predictive biomarkers of metastatic disease. Using patient peripheral blood polymorphonuclear neutrophils (PMNs), we identified that PCa progression dictates PMN cell surface markers and gene expression, but not cytotoxicity against PCa. Importantly, we also identified a novel phenomenon in which second generation androgen deprivation therapy (ADT) suppresses PMN cytotoxicity via increased transforming growth factor beta receptor I (TβRI). High dose testosterone and genetic or pharmacologic TβRI inhibition rescued androgen receptor-mediated neutrophil suppression and restored neutrophil anti-tumor immune response. These studies highlight the ability to leverage standard-care ADT to generate neutrophil anti-tumor responses against bone metastatic PCa.
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Affiliation(s)
- Massar Alsamraae
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Diane Costanzo-Garvey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Benjamin A Teply
- Fred & Pamela Buffett Cancer Center, Omaha, NE, USA; Division of Oncology & Hematology/Oncology, Department of Internal Medicine, University of Nebraska Medical Center Omaha, NE, USA
| | - Shawna Boyle
- Fred & Pamela Buffett Cancer Center, Omaha, NE, USA
| | | | | | | | - Alicia J Dafferner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Maher Y Abdalla
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rachel W Fallet
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Tammy Kielian
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Heather Jensen-Smith
- Fred & Pamela Buffett Cancer Center, Omaha, NE, USA; Eppley Institute for Research in Cancer and Allied Diseases, Omaha, NE, USA
| | - Edson I deOliveira
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Keqiang Chen
- Laboratory of Cancer Innovation, National Cancer Institute, Frederick, MD, USA
| | - Ian A Bettencourt
- Laboratory of Cancer Innovation, National Cancer Institute, Frederick, MD, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, National Cancer Institute, Frederick, MD, USA
| | - Daniel W McVicar
- Laboratory of Cancer Innovation, National Cancer Institute, Frederick, MD, USA
| | - Tyler Keeley
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fang Yu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Leah M Cook
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA; Fred & Pamela Buffett Cancer Center, Omaha, NE, USA.
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5
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Landa I, Thornton CEM, Xu B, Haase J, Krishnamoorthy GP, Hao J, Knauf JA, Herbert ZT, Martínez P, Blasco MA, Ghossein R, Fagin JA. Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects. Mol Cancer Res 2023; 21:1163-1175. [PMID: 37478162 DOI: 10.1158/1541-7786.mcr-23-0144] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Mutations in the promoter of the telomerase reverse transcriptase (TERT) gene are the paradigm of a cross-cancer alteration in a noncoding region. TERT promoter mutations (TPM) are biomarkers of poor prognosis in cancer, including thyroid tumors. TPMs enhance TERT transcription, which is otherwise silenced in adult tissues, thus reactivating a bona fide oncoprotein. To study TERT deregulation and its downstream consequences, we generated a Tert mutant promoter mouse model via CRISPR/Cas9 engineering of the murine equivalent locus (Tert-123C>T) and crossed it with thyroid-specific BrafV600E-mutant mice. We also employed an alternative model of Tert overexpression (K5-Tert). Whereas all BrafV600E animals developed well-differentiated papillary thyroid tumors, 29% and 36% of BrafV600E+Tert-123C>T and BrafV600E+K5-Tert mice progressed to poorly differentiated cancers at week 20, respectively. Tert-upregulated tumors showed increased mitosis and necrosis in areas of solid growth, and older animals displayed anaplastic-like features, that is, spindle cells and macrophage infiltration. Murine TPM increased Tert transcription in vitro and in vivo, but temporal and intratumoral heterogeneity was observed. RNA-sequencing of thyroid tumor cells showed that processes other than the canonical Tert-mediated telomere maintenance role operate in these specimens. Pathway analysis showed that MAPK and PI3K/AKT signaling, as well as processes not previously associated with this tumor etiology, involving cytokine, and chemokine signaling, were overactivated. These models constitute useful preclinical tools to understand the cell-autonomous and microenvironment-related consequences of Tert-mediated progression in advanced thyroid cancers and other aggressive tumors carrying TPMs. IMPLICATIONS Telomerase-driven cancer progression activates pathways that can be dissected and perhaps therapeutically exploited.
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Affiliation(s)
- Iñigo Landa
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Caitlin E M Thornton
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob Haase
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Gnana P Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jingzhu Hao
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jeffrey A Knauf
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paula Martínez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - María A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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6
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2023; 186:3476-3498.e35. [PMID: 37541199 PMCID: PMC10414761 DOI: 10.1016/j.cell.2023.07.004] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.
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Affiliation(s)
- Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Department of Population Health Science and Policy, Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jiayi Ji
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Uliana J Voytovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yajue Huang
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sun-Hee Lee
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Lindsay Bergan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David Fenyo
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua Wang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Mary Helen Barcellos-Hoff
- Helen Diller Family Comprehensive Cancer Center, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris J Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Charles Drescher
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Marcin Cieslik
- Department of Pathology, Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Michael J Birrer
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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7
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Klonowska K, Giannikou K, Grevelink JM, Boeszoermenyi B, Thorner AR, Herbert ZT, Afrin A, Treichel AM, Hamieh L, Kotulska K, Jozwiak S, Moss J, Darling TN, Kwiatkowski DJ. Comprehensive genetic and phenotype analysis of 95 individuals with mosaic tuberous sclerosis complex. Am J Hum Genet 2023; 110:979-988. [PMID: 37141891 PMCID: PMC10257004 DOI: 10.1016/j.ajhg.2023.04.002] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/12/2023] [Indexed: 05/06/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is a neurogenetic disorder due to loss-of-function TSC1 or TSC2 variants, characterized by tumors affecting multiple organs, including skin, brain, heart, lung, and kidney. Mosaicism for TSC1 or TSC2 variants occurs in 10%-15% of individuals diagnosed with TSC. Here, we report comprehensive characterization of TSC mosaicism by using massively parallel sequencing (MPS) of 330 TSC samples from a variety of tissues and fluids from a cohort of 95 individuals with mosaic TSC. TSC1 variants in individuals with mosaic TSC are much less common (9%) than in germline TSC overall (26%) (p < 0.0001). The mosaic variant allele frequency (VAF) is significantly higher in TSC1 than in TSC2, in both blood and saliva (median VAF: TSC1, 4.91%; TSC2, 1.93%; p = 0.036) and facial angiofibromas (median VAF: TSC1, 7.7%; TSC2 3.7%; p = 0.004), while the number of TSC clinical features in individuals with TSC1 and TSC2 mosaicism was similar. The distribution of mosaic variants across TSC1 and TSC2 is similar to that for pathogenic germline variants in general TSC. The systemic mosaic variant was not present in blood in 14 of 76 (18%) individuals with TSC, highlighting the value of analysis of multiple samples from each individual. A detailed comparison revealed that nearly all TSC clinical features are less common in individuals with mosaic versus germline TSC. A large number of previously unreported TSC1 and TSC2 variants, including intronic and large rearrangements (n = 11), were also identified.
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Affiliation(s)
- Katarzyna Klonowska
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Joannes M Grevelink
- Boston Dermatology and Laser Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Barbara Boeszoermenyi
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron R Thorner
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Antara Afrin
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA; Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alison M Treichel
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA; Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University Cleveland, Cleveland, OH 44106, USA
| | - Lana Hamieh
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hospital Medicine, Barnes Jewish Hospital, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw 04-736, Poland
| | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, Children's Memorial Health Institute, Warsaw 04-736, Poland; Research Department, Children's Memorial Health Institute, Warsaw 04-736, Poland
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas N Darling
- Department of Dermatology, Uniformed Services University, Bethesda, MA 20814, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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8
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Koch MS, Zdioruk M, Nowicki MO, Hoetker MS, Herbert ZT, Barone F, Tak PP, Chiocca EA, Tabatabai G, Lawler SE. Uncovering transcriptomic landscape alterations of CAN-2409 in in vitro and in vivo glioma models. Front Med (Lausanne) 2023; 10:1140352. [PMID: 37228396 PMCID: PMC10203593 DOI: 10.3389/fmed.2023.1140352] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023] Open
Abstract
Rationale CAN-2409 is a locally delivered oncolytic therapy, which results in vaccination against the injected tumor. CAN-2409 consists of a non-replicating adenovirus armed with the Herpes virus thymidine kinase, which metabolizes ganciclovir into a phosphorylated nucleotide that is incorporated into the tumor cell's genome, thereby inflicting immunogenic cancer cell death. While CAN-2409's immunological impact has been well characterized, its effects on the tumor cells transcriptome remains unknown. We compared the transcriptomic landscape after treatment of glioblastoma models with CAN-2409 in vitro and in vivo to assess how the interplay with the tumor microenvironment influences CAN-2409-mediated transcriptome alterations. Methods We performed RNA-Seq with CAN-2409 treated patient-derived glioma stem-like cells and tumors of C57/BL6 mice and compared KEGG pathway usage and differential gene expression focusing on immune cell and cytokine profiles. T-cell -killing assays were performed to assess candidate effectors. Results PCA analysis showed distinct clustering of control and CAN-2409 samples under both conditions. KEGG pathway analysis revealed significant enrichment for p53 signaling and cell cycle pathway, with similar dynamics for key regulators of both pathways in vitro and in vivo, including MYC, CCNB1, PLK1 and CDC20. Selected alterations (PLK1 and CCNB1) were validated at the protein level. Cytokine expression analysis revealed upregulation of pro-inflammatory IL12a under both conditions; immune cell gene profiling showed reduction of myeloid associated genes. T-cell-killing assays showed increased killing in the presence of IL-12. Conclusion CAN-2409 significantly alters the transcriptome both in vitro and in vivo. Comparison of pathway enrichment revealed mutual and differential utilization of pathways under both conditions, suggesting a modulating influence on the cell cycle in tumor cells, and of the tumor microenvironment on the transcriptome in vivo. IL-12 synthesis likely depends on interactions with the tumor microenvironment, and it facilitates CAN-2409 cell killing. This dataset provides potential to understand resistance mechanisms and identify potential biomarkers for future studies.
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Affiliation(s)
- Marilin S. Koch
- Harvey Cushing Neurooncology Research Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Mykola Zdioruk
- Harvey Cushing Neurooncology Research Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Michal O. Nowicki
- Harvey Cushing Neurooncology Research Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Michael S. Hoetker
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Zachary T. Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Paul P. Tak
- Candel Therapeutics, Needham, MA, United States
| | - E. Antonio Chiocca
- Harvey Cushing Neurooncology Research Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Ghazaleh Tabatabai
- Department of Neurology and Interdisciplinary Neuro-Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Sean E. Lawler
- Harvey Cushing Neurooncology Research Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Pathology and Laboratory Medicine, Legorreta Cancer Center, Brown University, Providence, RI, United States
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9
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Landa I, Thornton CEM, Xu B, Haase J, Krishnamoorthy GP, Hao J, Knauf JA, Herbert ZT, Blasco MA, Ghossein R, Fagin JA. Telomerase reactivation induces progression of mouse Braf V600E -driven thyroid cancers without telomere lengthening. bioRxiv 2023:2023.01.24.525280. [PMID: 36747657 PMCID: PMC9900760 DOI: 10.1101/2023.01.24.525280] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mutations in the promoter of the telomerase reverse transcriptase ( TERT ) gene are the paradigm of a cross-cancer alteration in a non-coding region. TERT promoter mutations (TPMs) are biomarkers of poor prognosis in several tumors, including thyroid cancers. TPMs enhance TERT transcription, which is otherwise silenced in adult tissues, thus reactivating a bona fide oncoprotein. To study TERT deregulation and its downstream consequences, we generated a Tert mutant promoter mouse model via CRISPR/Cas9 engineering of the murine equivalent locus (Tert -123C>T ) and crossed it with thyroid-specific Braf V600E -mutant mice. We also employed an alternative model of Tert overexpression (K5-Tert). Whereas all Braf V600E animals developed well-differentiated papillary thyroid tumors, 29% and 36% of Braf V600E +Tert -123C>T and Braf V600E +K5-Tert mice progressed to poorly differentiated thyroid cancers at week 20, respectively. Braf+Tert tumors showed increased mitosis and necrosis in areas of solid growth, and older animals from these cohorts displayed anaplastic-like features, i.e., spindle cells and macrophage infiltration. Murine Tert promoter mutation increased Tert transcription in vitro and in vivo , but temporal and intra-tumoral heterogeneity was observed. RNA-sequencing of thyroid tumor cells showed that processes other than the canonical Tert-mediated telomere maintenance role operate in these specimens. Pathway analysis showed that MAPK and PI3K/AKT signaling, as well as processes not previously associated with this tumor etiology, involving cytokine and chemokine signaling, were overactivated. Braf+Tert animals remained responsive to MAPK pathway inhibitors. These models constitute useful pre-clinical tools to understand the cell-autonomous and microenvironment-related consequences of Tert-mediated progression in advanced thyroid cancers and other aggressive tumors carrying TPMs.
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Affiliation(s)
- Iñigo Landa
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Caitlin EM Thornton
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacob Haase
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Gnana P. Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jingzhu Hao
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Knauf
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
| | - María A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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10
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Cassidy MF, Herbert ZT, Moulton VR. Splicing factor SRSF1 controls autoimmune-related molecular pathways in regulatory T cells distinct from FoxP3. Mol Immunol 2022; 152:140-152. [PMID: 36368121 DOI: 10.1016/j.molimm.2022.10.017] [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: 01/18/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
Regulatory T cells (Tregs) are vital for maintaining immune self-tolerance, and their impaired function leads to autoimmune disease. Mutations in FoxP3, the master transcriptional regulator of Tregs, leads to immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome in humans and the early lethal "scurfy" phenotype with multi-organ autoimmune disease in mice. We recently identified serine/arginine-rich splicing factor 1 (SRSF1) as an indispensable regulator of Treg homeostasis and function. Intriguingly, Treg-conditional SRSF1-deficient mice exhibit early lethal systemic autoimmunity with multi-organ inflammation reminiscent of the scurfy mice. Importantly, SRSF1 is decreased in T cells from patients with the autoimmune disease systemic lupus erythematosus (SLE), and low SRSF1 levels inversely correlate with disease severity. Given that the Treg-specific deficiency of SRSF1 causes similarly profound autoimmune disease outcomes in mice as the deficiency/mutation in FoxP3, we aimed to evaluate the genes and molecular pathways controlled by these two indispensable regulatory proteins. We performed comparative bioinformatic analyses of transcriptomic profiles of Tregs from Srsf1-knockout mice and two Foxp3 mutant mice--the FoxP3-deficient ΔFoxp3 and the Foxp3 M370I mutant mice. We identified 132 differentially expressed genes (DEGs) unique to Srsf1-ko Tregs, 503 DEGs unique to Foxp3 M370I Tregs, and 1367 DEGs unique to ΔFoxp3 Tregs. Gene set enrichment and pathway analysis of DEGs unique to Srsf1-ko Tregs indicate that SRSF1 controls cytokine and immune response pathways. Conversely, FoxP3 controls pathways involved in DNA replication and cell cycle. Besides the distinct gene signatures, we identified only 30 shared genes between all three Treg mutants, mostly contributing to cytokine and immune defense pathways. Prominent genes included the chemokines CXCR6 and CCL1 and the checkpoint inhibitors FASLG and PDCD1. Thus, we demonstrate that SRSF1 and FoxP3 control common and distinct molecular pathways implicated in autoimmunity. Our analyses suggest that SRSF1 controls crucial immune functions in Tregs contributing to immune tolerance, and perturbations in its levels lead to systemic autoimmunity via mechanisms that are largely distinct from FoxP3.
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Affiliation(s)
- Michael F Cassidy
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States; Tufts University School of Medicine, Boston, MA, United States.
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Vaishali R Moulton
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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11
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Juarez I, Su S, Herbert ZT, Teijaro JR, Moulton VR. Splicing factor SRSF1 is essential for CD8 T cell function and host antigen-specific viral immunity. Front Immunol 2022; 13:906355. [PMID: 36189299 PMCID: PMC9523749 DOI: 10.3389/fimmu.2022.906355] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Cytotoxic CD8 T cells are crucial for the host antigen-specific immune response to viral pathogens. Here we report the identification of an essential role for the serine/arginine-rich splicing factor (SRSF) 1 in CD8 T cell homeostasis and function. Specifically, SRSF1 is necessary for the maintenance of normal CD8 T lymphocyte numbers in the lymphoid compartment, and for the proliferative capacity and cytotoxic function of CD8 T cells. Furthermore, SRSF1 is required for antigen-specific IFN-γ cytokine responses in a viral infection challenge in mice. Transcriptomics analyses of Srsf1-deficient T cells reveal that SRSF1 controls proliferation, MAP kinase signaling and IFN signaling pathways. Mechanistically, SRSF1 controls the expression and activity of the Mnk2/p38-MAPK axis at the molecular level. Our findings reveal previously unrecognized roles for SRSF1 in the physiology and function of cytotoxic CD8 T lymphocytes and a potential molecular mechanism in viral immunopathogenesis.
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Affiliation(s)
- Ignacio Juarez
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Department of Immunology, Ophthalmology and ENT, Faculty of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Shi Su
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Zachary T. Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, United States
| | - John R. Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Vaishali R. Moulton
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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12
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Canesin G, Feldbrügge L, Wei G, Janovicova L, Janikova M, Csizmadia E, Ariffin J, Hedblom A, Herbert ZT, Robson SC, Celec P, Swanson KD, Nasser I, Popov YV, Wegiel B. Heme oxygenase-1 mitigates liver injury and fibrosis via modulation of LNX1/Notch1 pathway in myeloid cells. iScience 2022; 25:104983. [PMID: 36093061 PMCID: PMC9450142 DOI: 10.1016/j.isci.2022.104983] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 01/12/2023] Open
Abstract
Activation of resident macrophages (Mϕ) and hepatic stellate cells is a key event in chronic liver injury. Mice with heme oxygenase-1 (HO-1; Hmox1)-deficient Mϕ (LysM-Cre:Hmox1 flfl ) exhibit increased inflammation, periportal ductular reaction, and liver fibrosis following bile duct ligation (BDL)-induced liver injury and increased pericellular fibrosis in NASH model. RiboTag-based RNA-sequencing profiling of hepatic HO-1-deficient Mϕ revealed dysregulation of multiple genes involved in lipid and amino acid metabolism, regulation of oxidative stress, and extracellular matrix turnover. Among these genes, ligand of numb-protein X1 (LNX1) expression is strongly suppressed in HO-1-deficient Mϕ. Importantly, HO-1 and LNX1 were expressed by hepatic Mϕ in human biliary and nonbiliary end-stage cirrhosis. We found that Notch1 expression, a downstream target of LNX1, was increased in LysM-Cre:Hmox1 flfl mice. In HO-1-deficient Mϕ treated with heme, transient overexpression of LNX1 drives M2-like Mϕ polarization. In summary, we identified LNX1/Notch1 pathway as a downstream target of HO-1 in liver fibrosis.
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Affiliation(s)
- Giacomo Canesin
- Department of Surgery, Division of Surgical Sciences, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Linda Feldbrügge
- Charité – Universitätsmedizin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Surgery, Campus Charité Mitte and Campus Virchow-Klinikum, 13353 Berlin, Germany,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Guangyan Wei
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA,Department of Radiation Oncology, First Affiliated Hospital, Sun Yat-sen University, 510080 Guangzhou, China
| | - Lubica Janovicova
- Department of Surgery, Division of Surgical Sciences, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA,Institute of Molecular Biomedicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Monika Janikova
- Department of Surgery, Division of Surgical Sciences, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA,Institute of Molecular Biomedicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Eva Csizmadia
- Department of Surgery, Division of Surgical Sciences, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Juliana Ariffin
- Department of Surgery, Division of Surgical Sciences, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Andreas Hedblom
- Department of Surgery, Division of Surgical Sciences, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Zachary T. Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Simon C. Robson
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Peter Celec
- Institute of Molecular Biomedicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Kenneth D. Swanson
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Imad Nasser
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yury V. Popov
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA,Corresponding author
| | - Barbara Wegiel
- Department of Surgery, Division of Surgical Sciences, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA,Corresponding author
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13
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Klonowska K, Grevelink JM, Giannikou K, Ogorek BA, Herbert ZT, Thorner AR, Darling TN, Moss J, Kwiatkowski DJ. Ultrasensitive profiling of UV mutations identifies thousands of subclinical facial tumors in tuberous sclerosis complex. J Clin Invest 2022; 132:155858. [PMID: 35358092 PMCID: PMC9106361 DOI: 10.1172/jci155858] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Tuberous Sclerosis Complex (TSC) is a neurogenetic syndrome due to loss-of-function mutations in TSC2 or TSC1, characterized by tumors at multiple body sites, including facial angiofibroma (FAF). Here, an ultrasensitive assessment of the extent and range of UV-induced mutations in TSC facial skin was performed. METHODS A Multiplex High-sensitivity PCR Assay (MHPA) was developed, enabling mutation detection at extremely low (<0.1%) variant allele frequencies (VAF). RESULTS MHPA assays were developed for both TSC2 and TP53, and applied to 81 samples, including 66 skin biopsies. UV-induced second hit mutation causing inactivation of TSC2 was pervasive in TSC facial skin with an average of 4.8 mutations per 2 mm biopsy at median VAF 0.08%, generating >150,000 incipient facial tumors (subclinical 'micro-FAFs') in the average TSC subject. The MHPA analysis also led to the identification of a refined UV-related indel signature and a recurrent complex mutation pattern, consisting of both a single or dinucleotide variant, and a 1-9 nt deletion, in cis. CONCLUSION TSC facial skin can be viewed as harboring a patchwork of clonal fibroblast proliferations (micro-FAF) with indolent growth, a small proportion of which develop into clinically observable FAF. Our observations also expand the spectrum of UV-related mutation signatures. FUNDING This work was supported by the TSC Alliance, Engles Family Fund for Research in TSC and LAM, and National Institutes of Health, National Heart, Lung, and Blood Institute [U01HL131022-04; Intramural Research Program].
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Affiliation(s)
- Katarzyna Klonowska
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Joannes M Grevelink
- Boston Dermatology and Laser Center, Massachusetts General Hospital, Boston, United States of America
| | - Krinio Giannikou
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Barbara A Ogorek
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, United States of America
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, United States of America
| | - Thomas N Darling
- Department of Dermatology, Uniformed Services University, Bethesda, United States of America
| | - Joel Moss
- Pulmonary Branch, National Heart Lung and Blood Institute, NIH, Bethesda, United States of America
| | - David J Kwiatkowski
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
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14
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Harada T, Heshmati Y, Kalfon J, Perez MW, Xavier Ferrucio J, Ewers J, Hubbell Engler B, Kossenkov A, Ellegast JM, Yi JS, Bowker A, Zhu Q, Eagle K, Liu T, Kai Y, Dempster JM, Kugener G, Wickramasinghe J, Herbert ZT, Li CH, Vrabič Koren J, Weinstock DM, Paralkar VR, Nabet B, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia. Genes Dev 2022; 36:368-389. [PMID: 35301220 PMCID: PMC8973843 DOI: 10.1101/gad.349284.121] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
In this study, Harada et al. identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. This study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes. Acute myeloid leukemia with KMT2A (MLL) rearrangements is characterized by specific patterns of gene expression and enhancer architecture, implying unique core transcriptional regulatory circuitry. Here, we identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. Rapid transcription factor degradation followed by measurements of genome-wide transcription rates and superresolution microscopy revealed that MEF2D and IRF8 form a distinct core regulatory module with a narrow direct transcriptional program that includes activation of the key oncogenes MYC, HOXA9, and BCL2. Our study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.
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Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Monika W Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Juliana Xavier Ferrucio
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Benjamin Hubbell Engler
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | | | - Jana M Ellegast
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joanna S Yi
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Allyson Bowker
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Qian Zhu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Ken Eagle Consulting, Houston, Texas 77494, USA
| | - Tianxin Liu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yan Kai
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Joshua M Dempster
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Guillaume Kugener
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Zachary T Herbert
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | | | - David M Weinstock
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Vikram R Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Charles Y Lin
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Neekesh V Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02215, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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15
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Xie Y, Kuan AT, Wang W, Herbert ZT, Mosto O, Olukoya O, Adam M, Vu S, Kim M, Tran D, Gómez N, Charpentier C, Sorour I, Lacey TE, Tolstorukov MY, Sabatini BL, Lee WCA, Harwell CC. Astrocyte-neuron crosstalk through Hedgehog signaling mediates cortical synapse development. Cell Rep 2022; 38:110416. [PMID: 35196485 PMCID: PMC8962654 DOI: 10.1016/j.celrep.2022.110416] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 05/12/2021] [Revised: 11/04/2021] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Neuron-glia interactions play a critical role in the regulation of synapse formation and circuit assembly. Here we demonstrate that canonical Sonic hedgehog (Shh) pathway signaling in cortical astrocytes acts to coordinate layer-specific synaptic connectivity. We show that the Shh receptor Ptch1 is expressed by cortical astrocytes during development and that Shh signaling is necessary and sufficient to promote the expression of genes involved in regulating synaptic development and layer-enriched astrocyte molecular identity. Loss of Shh in layer V neurons reduces astrocyte complexity and coverage by astrocytic processes in tripartite synapses; conversely, cell-autonomous activation of Shh signaling in astrocytes promotes cortical excitatory synapse formation. Furthermore, Shh-dependent genes Lrig1 and Sparc distinctively contribute to astrocyte morphology and synapse formation. Together, these results suggest that Shh secreted from deep-layer cortical neurons acts to specialize the molecular and functional features of astrocytes during development to shape circuit assembly and function. Xie et al. show that Sonic hedgehog expressed by cortical layer V neurons signals to Ptch1-expressing astrocytes where it is necessary to promote the expression of layer-enriched astrocyte gene networks that control synapse formation and astrocyte morphological complexity.
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Affiliation(s)
- Yajun Xie
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron T Kuan
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Wengang Wang
- Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Olivia Mosto
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Olubusola Olukoya
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Manal Adam
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Steve Vu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Minsu Kim
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Diana Tran
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicolás Gómez
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Claire Charpentier
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ingie Sorour
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tiara E Lacey
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bernardo L Sabatini
- Howard Hughes Medical Institute, Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Wei-Chung Allen Lee
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Corey C Harwell
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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16
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Cassidy MF, Herbert ZT, Moulton VR. Splicing factor SRSF1 controls distinct molecular programs in regulatory and effector T cells implicated in systemic autoimmune disease. Mol Immunol 2022; 141:94-103. [PMID: 34839165 PMCID: PMC10797198 DOI: 10.1016/j.molimm.2021.11.008] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/15/2021] [Accepted: 11/07/2021] [Indexed: 12/30/2022]
Abstract
Systemic autoimmune diseases are characterized by hyperactive effector T cells (Teffs), aberrant cytokines and chemokines, and dysfunctional regulatory T cells (Tregs). We previously uncovered new roles for serine/arginine-rich splicing factor 1 (SRSF1) in the control of genes involved in T cell signaling and cytokine production in human T cells. SRSF1 levels are decreased in T cells from patients with systemic lupus erythematosus (SLE), and low levels correlate with severe disease. Moreover, T cell-conditional Srsf1-deficient mice recapitulate the autoimmune phenotype, exhibiting CD4 T cell hyperactivity, dysfunctional Tregs, systemic autoimmunity, and tissue inflammation. However, the role of SRSF1 in controlling molecular programs in Teffs and Tregs and how these pathways are implicated in autoimmunity is not known. Here, by comparative bioinformatics analysis, we demonstrate that SRSF1 controls largely distinct gene programs in Tregs and Teffs in vivo. SRSF1 regulates 189 differentially expressed genes (DEGs) unique to Tregs, 582 DEGs unique to Teffs, and 29 DEGs shared between both. Shared genes included IL-17A, IL-17F, CSF1, CXCL10, and CXCR4, and were highly enriched for inflammatory response and cytokine-cytokine receptor interaction pathways. SRSF1 controls distinct pathways in Tregs, which include chemokine signaling and immune cell differentiation, compared with pathways in Teffs, which include cytokine production, T cell homeostasis, and activation. We identified putative mRNA binding targets of SRSF1 which include CSF1, CXCL10, and IL-17F. Finally, comparisons with transcriptomics profiles from lupus-prone MRL/lpr mice reveal that SRSF1 controls genes and pathways implicated in autoimmune disease. The target genes of SRSF1 and putative binding targets we discovered, have known roles in systemic autoimmunity. Our findings suggest that SRSF1 controls distinct molecular pathways in Tregs and Teffs and aberrant SRSF1 levels may contribute to their dysfunction and immunopathogenesis of systemic autoimmune disease.
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Affiliation(s)
- Michael F Cassidy
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States; Tufts University School of Medicine, Boston, MA, United States
| | - Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, United States
| | - Vaishali R Moulton
- Division of Rheumatology and Clinical Immunology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.
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17
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Huang D, Chowdhury S, Wang H, Savage SR, Ivey RG, Kennedy JJ, Whiteaker JR, Lin C, Hou X, Oberg AL, Larson MC, Eskandari N, Delisi DA, Gentile S, Huntoon CJ, Voytovich UJ, Shire ZJ, Yu Q, Gygi SP, Hoofnagle AN, Herbert ZT, Lorentzen TD, Calinawan A, Karnitz LM, Weroha SJ, Kaufmann SH, Zhang B, Wang P, Birrer MJ, Paulovich AG. Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. Cell Rep Med 2021; 2:100471. [PMID: 35028612 PMCID: PMC8714940 DOI: 10.1016/j.xcrm.2021.100471] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 12/18/2020] [Revised: 09/24/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
Resistance to platinum compounds is a major determinant of patient survival in high-grade serous ovarian cancer (HGSOC). To understand mechanisms of platinum resistance and identify potential therapeutic targets in resistant HGSOC, we generated a data resource composed of dynamic (±carboplatin) protein, post-translational modification, and RNA sequencing (RNA-seq) profiles from intra-patient cell line pairs derived from 3 HGSOC patients before and after acquiring platinum resistance. These profiles reveal extensive responses to carboplatin that differ between sensitive and resistant cells. Higher fatty acid oxidation (FAO) pathway expression is associated with platinum resistance, and both pharmacologic inhibition and CRISPR knockout of carnitine palmitoyltransferase 1A (CPT1A), which represents a rate limiting step of FAO, sensitize HGSOC cells to platinum. The results are further validated in patient-derived xenograft models, indicating that CPT1A is a candidate therapeutic target to overcome platinum resistance. All multiomic data can be queried via an intuitive gene-query user interface (https://sites.google.com/view/ptrc-cell-line).
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Affiliation(s)
- Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hong Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sara R. Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaonan Hou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ann L. Oberg
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Melissa C. Larson
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN 55905, USA
| | - Najmeh Eskandari
- Division of Hematology and Oncology, Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Davide A. Delisi
- Division of Hematology and Oncology, Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Saverio Gentile
- Division of Hematology and Oncology, Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | | | - Uliana J. Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Zahra J. Shire
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew N. Hoofnagle
- Department of Lab Medicine, University of Washington, Seattle, WA 98195, USA
| | - Zachary T. Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - S. John Weroha
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael J. Birrer
- University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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18
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Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol 2021; 39:1466. [PMID: 34635840 DOI: 10.1038/s41587-021-01122-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W Tighe
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Charles M Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Michael M Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Phoebe K Laaguiby
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derek Warner
- DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA
| | - George S Grills
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenny Xiang
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Xia Zhao
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yonggang Zhao
- BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | | | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Don A Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. .,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. .,The Feil Family Brain and Mind Research Institute, New York, NY, USA. .,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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19
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Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. Nat Biotechnol 2021; 39:1129-1140. [PMID: 34504351 PMCID: PMC8985210 DOI: 10.1038/s41587-021-01049-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2 × 250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.
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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W. Tighe
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Charles M. Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Phoebe K. Laaguiby
- University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA
| | - Zachary T. Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derek Warner
- DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Jin Jen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenny Xiang
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Xia Zhao
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yonggang Zhao
- BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | | | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
| | - Don A. Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.,The Feil Family Brain and Mind Research Institute, New York, NY, USA.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.,Correspondence and requests for materials should be addressed to Fritz J. Sedlazeck, Don A. Baldwin or Christopher E. Mason. ; ;
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20
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Ratnapriya S, Harris M, Chov A, Herbert ZT, Vrbanac V, Deruaz M, Achuthan V, Engelman AN, Sodroski J, Herschhorn A. Intra- and extra-cellular environments contribute to the fate of HIV-1 infection. Cell Rep 2021; 36:109622. [PMID: 34469717 PMCID: PMC8463096 DOI: 10.1016/j.celrep.2021.109622] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/07/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
HIV-1 entry into host cells leads to one of the following three alternative fates: (1) HIV-1 elimination by restriction factors, (2) establishment of HIV-1 latency, or (3) active viral replication in target cells. Here, we report the development of an improved system for monitoring HIV-1 fate at single-cell and population levels and show the diverse applications of this system to study specific aspects of HIV-1 fate in different cell types and under different environments. An analysis of the transcriptome of infected, primary CD4+ T cells that support alternative fates of HIV-1 identifies differential gene expression signatures in these cells. Small molecules are able to selectively target cells that support viral replication with no significant effect on viral latency. In addition, HIV-1 fate varies in different tissues following infection of humanized mice in vivo. Altogether, these studies indicate that intra- and extra-cellular environments contribute to the fate of HIV-1 infection.
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Affiliation(s)
- Sneha Ratnapriya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Miranda Harris
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Angela Chov
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Vladimir Vrbanac
- Humanized Immune System Mouse Program, Ragon Institute of MGH, MIT and Harvard, and Center for Immunology and Inflammatory Disease, Cambridge, MA 02139, USA
| | - Maud Deruaz
- Humanized Immune System Mouse Program, Ragon Institute of MGH, MIT and Harvard, and Center for Immunology and Inflammatory Disease, Cambridge, MA 02139, USA
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
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21
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Podnar JW, Pantano L, Zeller MJ, Kolling FW, Zhang Y, Alekseyev YO, Niece J, Deiderick H, Fan J, Xuei X, Kieleczawa J, Levine SS, Herbert ZT, Adams M. Cross-Site Evaluation of Commercial Sanger Sequencing Chemistries. J Biomol Tech 2021; 31:88-93. [PMID: 32831655 DOI: 10.7171/jbt.20-3103-002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sanger sequencing remains an essential tool utilized by researchers. Despite competition from commercial sequencing providers, many academic sequencing core facilities continue to offer these services based on a model of competitive pricing, knowledgeable technical support, and rapid turnaround time. In-house Sanger sequencing remains a viable core service and, until recently, Applied Biosystems BigDye Terminator chemistry was the only commercially available solution for Sanger DNA sequencing on Applied Biosystems (ABI) instruments; however, several new products employing novel dye chemistries and reaction configurations have entered the market. As a result, there is a need to benchmark the performance of these new chemistries on various DNA templates, including difficult-to-sequence templates, and their amenability to commonly employed cost-saving measures, such as dye dilution and reaction miniaturization. To evaluate these new reagents, a study was designed to compare the quality of Sanger sequencing data produced by ABI BigDye and commercially available kits from 2 other vendors using both control and difficult-to-sequence DNA templates under various reaction conditions. This study will serve as a valuable resource to core facilities conducting Sanger sequencing that wish to evaluate the use of an alternative chemistry in their sequencing core.
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Affiliation(s)
- Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Lorena Pantano
- eGenesis Engineering Life, Cambridge, Massachusetts, USA
| | - Molly J Zeller
- DNA Sequencing Facility, University of Wisconsin Biotechnology Center, Madison, Wisconsin, USA
| | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Yanping Zhang
- Gene Expression and Genotyping, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jeremy Niece
- DNA Sequencing Facility, University of Wisconsin Biotechnology Center, Madison, Wisconsin, USA
| | - Heather Deiderick
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Jun Fan
- Department of Biomedical Sciences, Genomic Core Facility, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
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22
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Herbert ZT, Thimmapuram J, Xie S, Kershner JP, Kolling FW, Ringelberg CS, LeClerc A, Alekseyev YO, Fan J, Podnar JW, Stevenson HS, Sommerville G, Gupta S, Berkeley M, Koeman J, Perera A, Scott AR, Grenier JK, Malik J, Ashton JM, Pivarski KL, Wang X, Kuffel G, Mesa TE, Smith AT, Shen J, Takata Y, Volkert TL, Love JA, Zhang Y, Wang J, Xuei X, Adams M, Levine SS. Multisite Evaluation of Next-Generation Methods for Small RNA Quantification. J Biomol Tech 2021; 31:47-56. [PMID: 31966025 DOI: 10.7171/jbt.20-3102-001] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Small RNAs (smRNAs) are important regulators of many biologic processes and are now most frequently characterized using Illumina sequencing. However, although standard RNA sequencing library preparation has become routine in most sequencing facilities, smRNA sequencing library preparation has historically been challenging because of high input requirements, laborious protocols involving gel purifications, inability to automate, and a lack of benchmarking standards. Additionally, studies have suggested that many of these methods are nonlinear and do not accurately reflect the amounts of smRNAs in vivo. Recently, a number of new kits have become available that permit lower input amounts and less laborious, gel-free protocol options. Several of these new kits claim to reduce RNA ligase-dependent sequence bias through novel adapter modifications and to lessen adapter-dimer contamination in the resulting libraries. With the increasing number of smRNA kits available, understanding the relative strengths of each method is crucial for appropriate experimental design. In this study, we systematically compared 9 commercially available smRNA library preparation kits as well as NanoString probe hybridization across multiple study sites. Although several of the new methodologies do reduce the amount of artificially over- and underrepresented microRNAs (miRNAs), we observed that none of the methods was able to remove all of the bias in the library preparation. Identical samples prepared with different methods show highly varied levels of different miRNAs. Even so, many methods excelled in ease of use, lower input requirement, fraction of usable reads, and reproducibility across sites. These differences may help users select the most appropriate methods for their specific question of interest.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Carol S Ringelberg
- Genomics and Molecular Biology Shared Resource, Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, Massachusetts, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Holly S Stevenson
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, Texas, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shipra Gupta
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Julie Koeman
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Allison R Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jennifer K Grenier
- RNA Sequencing Core, Department of Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Jeffrey Malik
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, New York, USA
| | - Kara L Pivarski
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Xinkun Wang
- NUSeq Core Research Facility, Northwestern University, Chicago, Illinois, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Loyola University Chicago, Maywood, Illinois, USA
| | - Tania E Mesa
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew T Smith
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, Texas, USA
| | - Thomas L Volkert
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jennifer A Love
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research Gene Expression and Genotyping, University of Florida, Gainsville, Florida, USA
| | - Jun Wang
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana, USA; and
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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23
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Feng Y, Mischler WJ, Gurung AC, Kavanagh TR, Androsov G, Sadow PM, Herbert ZT, Priolo C. Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis. Cancer Res 2020; 80:2751-2763. [PMID: 32393662 DOI: 10.1158/0008-5472.can-19-2884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/16/2019] [Revised: 03/25/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022]
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominant disease characterized by multiorgan hamartomas, including renal angiomyolipomas and pulmonary lymphangioleiomyomatosis (LAM). TSC2 deficiency leads to hyperactivation of mTOR Complex 1 (mTORC1), a master regulator of cell growth and metabolism. Phospholipid metabolism is dysregulated upon TSC2 loss, causing enhanced production of lysophosphatidylcholine (LPC) species by TSC2-deficient tumor cells. LPC is the major substrate of the secreted lysophospholipase D autotaxin (ATX), which generates two bioactive lipids, lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P). We report here that ATX expression is upregulated in human renal angiomyolipoma-derived TSC2-deficient cells compared with TSC2 add-back cells. Inhibition of ATX via the clinically developed compound GLPG1690 suppressed TSC2-loss associated oncogenicity in vitro and in vivo and induced apoptosis in TSC2-deficient cells. GLPG1690 suppressed AKT and ERK1/2 signaling and profoundly impacted the transcriptome of these cells while inducing minor gene expression changes in TSC2 add-back cells. RNA-sequencing studies revealed transcriptomic signatures of LPA and S1P, suggesting an LPA/S1P-mediated reprogramming of the TSC lipidome. In addition, supplementation of LPA or S1P rescued proliferation and viability, neutral lipid content, and AKT or ERK1/2 signaling in human TSC2-deficient cells treated with GLPG1690. Importantly, TSC-associated renal angiomyolipomas have higher expression of LPA receptor 1 and S1P receptor 3 compared with normal kidney. These studies increase our understanding of TSC2-deficient cell metabolism, leading to novel potential therapeutic opportunities for TSC and LAM. SIGNIFICANCE: This study identifies activation of the ATX-LPA/S1P pathway as a novel mode of metabolic dysregulation upon TSC2 loss, highlighting critical roles for ATX in TSC2-deficient cell fitness and in TSC tumorigenesis.
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Affiliation(s)
- You Feng
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - William J Mischler
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Ashish C Gurung
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Taylor R Kavanagh
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Grigoriy Androsov
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Peter M Sadow
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Zachary T Herbert
- Harvard Medical School, Boston, Massachusetts
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Carmen Priolo
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
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24
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Oser MG, Sabet AH, Gao W, Chakraborty AA, Schinzel AC, Jennings RB, Fonseca R, Bonal DM, Booker MA, Flaifel A, Novak JS, Christensen CL, Zhang H, Herbert ZT, Tolstorukov MY, Buss EJ, Wong KK, Bronson RT, Nguyen QD, Signoretti S, Kaelin WG. The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis. Genes Dev 2019; 33:1718-1738. [PMID: 31727771 PMCID: PMC6942053 DOI: 10.1101/gad.328336.119] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [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: 05/02/2019] [Accepted: 10/21/2019] [Indexed: 01/08/2023]
Abstract
More than 90% of small cell lung cancers (SCLCs) harbor loss-of-function mutations in the tumor suppressor gene RB1 The canonical function of the RB1 gene product, pRB, is to repress the E2F transcription factor family, but pRB also functions to regulate cellular differentiation in part through its binding to the histone demethylase KDM5A (also known as RBP2 or JARID1A). We show that KDM5A promotes SCLC proliferation and SCLC's neuroendocrine differentiation phenotype in part by sustaining expression of the neuroendocrine transcription factor ASCL1. Mechanistically, we found that KDM5A sustains ASCL1 levels and neuroendocrine differentiation by repressing NOTCH2 and NOTCH target genes. To test the role of KDM5A in SCLC tumorigenesis in vivo, we developed a CRISPR/Cas9-based mouse model of SCLC by delivering an adenovirus (or an adeno-associated virus [AAV]) that expresses Cre recombinase and sgRNAs targeting Rb1, Tp53, and Rbl2 into the lungs of Lox-Stop-Lox Cas9 mice. Coinclusion of a KDM5A sgRNA decreased SCLC tumorigenesis and metastasis, and the SCLCs that formed despite the absence of KDM5A had higher NOTCH activity compared to KDM5A +/+ SCLCs. This work establishes a role for KDM5A in SCLC tumorigenesis and suggests that KDM5 inhibitors should be explored as treatments for SCLC.
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Affiliation(s)
- Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA
| | - Amin H Sabet
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Wenhua Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA
| | - Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA
| | - Anna C Schinzel
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Rebecca B Jennings
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA
| | - Raquel Fonseca
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Dennis M Bonal
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02210, USA
| | - Matthew A Booker
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Abdallah Flaifel
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA
| | - Jesse S Novak
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA
| | - Camilla L Christensen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Hua Zhang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York 10016, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Elizabeth J Buss
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Kwok-Kin Wong
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York 10016, USA
| | - Roderick T Bronson
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02215
| | - Quang-De Nguyen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02210, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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25
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Reitman ZJ, Paolella B, Bergthold G, Pelton K, Jones R, Becker S, Sinai CE, Malkin H, Huang Y, Grimmett L, Herbert ZT, Sun Y, Weatherbee J, Alberta J, Daley J, Rozenblatt-Rosen O, Segal R, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles C, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Abstract 3647: Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3647] [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
Single-cell RNA sequencing (scRNAseq) has been performed across a range of intermediate to high-grade gliomas that each harbor multiple driver mutations. Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma. PAs frequently harbor oncogenic KIAA1549-BRAF fusions, and exhibit low rates of other driver mutations. While PAs exhibit a favorable prognosis compared to the higher-grade gliomas, treatment morbidity and tumor recurrence can represent major challenges for some PA patients. We performed scRNAseq of both tumor and non-tumor cells in newly-diagnosed PAs that contained KIAA1549-BRAF rearrangements. To confidently distinguish tumor cells from nontumor cells, we sorted cells by glial progenitor marker A2B5 status and profiled KIAA1549-BRAF fusion status of cells using a sensitive quantitative PCR-based assay. Results were validated using RNA in situ hybridization. When compared to higher-grade gliomas, a higher proportion of the PA tumor cells exhibited a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibited a progenitor-like phenotype with evidence of proliferation. These progenitor-like tumor cells expressed a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Similar patterns of expression of genes associated with the astrocyte-like and MAPK gene programs were also seen in formalin fixed, paraffin embedded PA tissues using RNA in situ hybridization. Immune cells, especially microglia, comprised almost half of all cells in the PAs and accounted for differences in bulk expression profiles between tumor locations and subtypes. These single cell transcriptional data reveal a transcriptional developmental hierarchy in a pediatric low grade glioma that is skewed towards more mature brain cells compared to higher-grade gliomas. The results indicate that future analyses of bulk PA tissues should attempt to account for considerable infiltration by nontumor cells. Finally, the finding that a MAPK gene program is not uniformly expressed in PA tumor cells has implications for ongoing clinical investigations of therapies directed at the MAPK pathway for the treatment of PA.
Citation Format: Zachary J. Reitman, Brenton Paolella, Guillaume Bergthold, Kristine Pelton, Robert Jones, Sarah Becker, Claire E. Sinai, Haley Malkin, Ying Huang, Leslie Grimmett, Zachary T. Herbert, Yu Sun, Jessica Weatherbee, John Alberta, John Daley, Orit Rozenblatt-Rosen, Rosalind Segal, Daphne Haas-Kogan, Mariella G. Filbin, Mario L. Suva, Aviv Regev, Charles Stiles, Mark W. Kieran, Liliana Goumnerova, Keith L. Ligon, Alex K. Shalek, Pratiti Bandopadhayay, Rameen Beroukhim. Single cell RNA sequencing reveals mitogenic and progenitor gene programs inBRAF-rearranged pilocytic astrocytomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3647.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ying Huang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Yu Sun
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - John Daley
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Aviv Regev
- 2Broad Institute of Harvard and MIT, Cambridge, MA
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26
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Chakraborty AA, Laukka T, Myllykoski M, Ringel AE, Booker MA, Tolstorukov MY, Meng YJ, Meier SR, Jennings RB, Creech AL, Herbert ZT, McBrayer SK, Olenchock BA, Jaffe JD, Haigis MC, Beroukhim R, Signoretti S, Koivunen P, Kaelin WG. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science 2019; 363:1217-1222. [PMID: 30872525 DOI: 10.1126/science.aaw1026] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
Abstract
Oxygen sensing is central to metazoan biology and has implications for human disease. Mammalian cells express multiple oxygen-dependent enzymes called 2-oxoglutarate (OG)-dependent dioxygenases (2-OGDDs), but they vary in their oxygen affinities and hence their ability to sense oxygen. The 2-OGDD histone demethylases control histone methylation. Hypoxia increases histone methylation, but whether this reflects direct effects on histone demethylases or indirect effects caused by the hypoxic induction of the HIF (hypoxia-inducible factor) transcription factor or the 2-OG antagonist 2-hydroxyglutarate (2-HG) is unclear. Here, we report that hypoxia promotes histone methylation in a HIF- and 2-HG-independent manner. We found that the H3K27 histone demethylase KDM6A/UTX, but not its paralog KDM6B, is oxygen sensitive. KDM6A loss, like hypoxia, prevented H3K27 demethylation and blocked cellular differentiation. Restoring H3K27 methylation homeostasis in hypoxic cells reversed these effects. Thus, oxygen directly affects chromatin regulators to control cell fate.
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Affiliation(s)
- Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Tuomas Laukka
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, FIN-90014 Oulu, Finland
| | - Matti Myllykoski
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, FIN-90014 Oulu, Finland
| | - Alison E Ringel
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew A Booker
- Department of Informatics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Michael Y Tolstorukov
- Department of Informatics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Yuzhong Jeff Meng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,The Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel R Meier
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Rebecca B Jennings
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda L Creech
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zachary T Herbert
- Molecular Biology Core Facility, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Samuel K McBrayer
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Benjamin A Olenchock
- Division of Cardiovascular Medicine, Department of Medicine, The Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, FIN-90014 Oulu, Finland.
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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27
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Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS. Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction. BMC Genomics 2018; 19:199. [PMID: 29703133 PMCID: PMC6389247 DOI: 10.1186/s12864-018-4585-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/08/2018] [Indexed: 01/23/2023] Open
Abstract
Background Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. Results We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. Conclusions These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. Electronic supplementary material The online version of this article (10.1186/s12864-018-4585-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachary T Herbert
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jamie P Kershner
- BioFrontiers Institute, Next-Gen Sequencing Facility, University of Colorado Boulder, Boulder, CO, USA
| | - Vincent L Butty
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Yuriy O Alekseyev
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, MA, USA.,Department of Pathology and Laboratory Medicine, Boston University, Boston, MA, USA
| | - Jun Fan
- Genomic Core Facility, Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, USA
| | - Jessica W Podnar
- Genomic Sequencing and Analysis Facility, University of Texas, Austin, TX, USA
| | - Edward Wilcox
- DNA Sequencing Center, Brigham Young University, Provo, UT, USA
| | - Jenny Gipson
- Laboratory for Molecular Biology and Cytometry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Allison Gillaspy
- Laboratory for Molecular Biology and Cytometry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Krystalynne Morris
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Maura Berkeley
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashley LeClerc
- Microarray and Sequencing Resource Core Facility, Boston University, Boston, MA, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Gary Sommerville
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leslie Grimmett
- Molecular Biology Core Facilities at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Institute, Grand Rapids, MI, USA
| | - Stuart S Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Pomerantz MM, Spisák S, Jia L, Cronin AM, Csabai I, Ledet E, Sartor AO, Rainville I, O'Connor EP, Herbert ZT, Szállási Z, Oh WK, Kantoff PW, Garber JE, Schrag D, Kibel AS, Freedman ML. The association between germline BRCA2 variants and sensitivity to platinum-based chemotherapy among men with metastatic prostate cancer. Cancer 2017; 123:3532-3539. [PMID: 28608931 PMCID: PMC5802871 DOI: 10.1002/cncr.30808] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [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: 02/13/2017] [Revised: 04/11/2017] [Accepted: 04/19/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Breast cancer 2 (BRCA2)-associated breast and ovarian cancers are sensitive to platinum-based chemotherapy. It is unknown whether BRCA2-associated prostate cancer responds favorably to such treatment. METHODS A retrospective analysis of a single-institution cohort of men with castration-resistant, metastatic prostate cancer was performed to determine the association between carrier status of pathogenic BRCA2 germline variants and prostate-specific antigen response to carboplatin-based chemotherapy. From 2001 through 2015, 8081 adult men with prostate cancer who had a consultation and/or underwent treatment at Dana-Farber Cancer Institute provided blood samples and consented to analyses of biologic material and clinical records. A subgroup of 141 men received at least 2 doses of carboplatin and docetaxel for castration-resistant disease (94% were also taxane refractory). These patients were categorized according to the absence or presence of pathogenic germline mutations in BRCA2 based on DNA sequencing from whole blood. The primary outcome was the response rate to carboplatin/docetaxel chemotherapy, defined according to a decline in prostate-specific antigen that exceeded 50% within 12 weeks of initiating this regimen. Associations between BRCA2 mutation status and response to carboplatin-based chemotherapy were tested using the Fisher exact test, with a 2-sided P value < .05 as the threshold for significance. RESULTS Pathogenic germline BRCA2 variants were observed in 8 of 141 men (5.7%; 95% confidence interval, 2.5%-10.9%). Six of 8 BRCA2 carriers (75%) experienced prostate-specific antigen declines >50% within 12 weeks, compared with 23 of 133 noncarriers (17%; absolute difference, 58%; 95% confidence interval, 27%-88%; P < .001). Prostate cancer cell lines functionally corroborated these clinical findings. CONCLUSIONS BRCA2-associated, castration-resistant prostate cancer is associated with a higher likelihood of response to carboplatin-based chemotherapy than non-BRCA2-associated prostate cancer. Cancer 2017;123:3532-9. © 2017 American Cancer Society.
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Affiliation(s)
- Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sandor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Li Jia
- Department of Surgery, Division of Urology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Angel M Cronin
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Istvan Csabai
- Department of Physics of Complex Systems Eotvos Lorand University, Budapest, Hungary
| | - Elisa Ledet
- Department of Medicine, Tulane Cancer Center, New Orleans, Louisiana
| | - A Oliver Sartor
- Department of Medicine, Tulane Cancer Center, New Orleans, Louisiana
| | - Irene Rainville
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edward P O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zachary T Herbert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zoltan Szállási
- Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts
| | - William K Oh
- Department of Medicine, Division of Hematology and Oncology, Tisch Cancer Institute, New York, New York
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Institute, New York, New York
| | - Judy E Garber
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deborah Schrag
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Adam S Kibel
- Department of Surgery, Division of Urology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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29
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Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeay S, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell 2016; 30:183. [PMID: 27479034 DOI: 10.1016/j.ccell.2016.06.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeay S, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell 2016; 29:574-586. [PMID: 27070704 PMCID: PMC5177991 DOI: 10.1016/j.ccell.2016.03.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/25/2016] [Accepted: 03/11/2016] [Indexed: 01/22/2023]
Abstract
More than 90% of drugs with preclinical activity fail in human trials, largely due to insufficient efficacy. We hypothesized that adequately powered trials of patient-derived xenografts (PDX) in mice could efficiently define therapeutic activity across heterogeneous tumors. To address this hypothesis, we established a large, publicly available repository of well-characterized leukemia and lymphoma PDXs that undergo orthotopic engraftment, called the Public Repository of Xenografts (PRoXe). PRoXe includes all de-identified information relevant to the primary specimens and the PDXs derived from them. Using this repository, we demonstrate that large studies of acute leukemia PDXs that mimic human randomized clinical trials can characterize drug efficacy and generate transcriptional, functional, and proteomic biomarkers in both treatment-naive and relapsed/refractory disease.
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Affiliation(s)
- Elizabeth C Townsend
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Mark A Murakami
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Alexandra Christodoulou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Amanda L Christie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Johannes Köster
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tiffany A DeSouza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Scott P Kallgren
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Huiyun Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Shuo-Chieh Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Olivia Plana
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Joan Montero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Kristen E Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prakash Rao
- Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Raga Vadhi
- Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Michael Andreeff
- Leukemia Division, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philippe Armand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Karen K Ballen
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Patrizia Barzaghi-Rinaudo
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Sarah Cahill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vesselina G Cooke
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - David M Dorfman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hilary Eaton
- Office of Research and Technology Ventures, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin L Ebert
- Department of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Julia Etchin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brant Firestone
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - David C Fisher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Arnold S Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Ilene A Galinsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Hui Gao
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | | | - Timothy A Graubert
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ensar Halilovic
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Zachary T Herbert
- Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven M Horwitz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Giorgio Inghirami
- Department of Pathology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Andrew M Intlekofer
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Moriko Ito
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Shai Izraeli
- Functional Genomics and Leukemia Research, Sheba Medical Center, Tel Hashomer and Tel Aviv University, Ramat Gan, 52621, Israel
| | - Eric D Jacobsen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Caron A Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Sébastien Jeay
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Irmela Jeremias
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistraße 25, 81377 Munich, Germany; Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Lindwurmstraße 4, 80337 Munich, Germany
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Raphael Koch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Marina Konopleva
- Leukemia Division, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nadja Kopp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Steven M Kornblau
- Leukemia Division, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Thomas S Kupper
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nicole R LeBoeuf
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ann S LaCasce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Emma Lees
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Loretta S Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Masato Murakami
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Markus Muschen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Samuel Y Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Oreofe O Odejide
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rachel R Paquette
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew E Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeremy A Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brent Shoji
- Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - David P Steensma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Jerome Tamburini
- Université Paris Descartes, Faculté de Médecine Sorbonne Paris Cité, 75005 Paris, France
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul van Hummelen
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martha Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Marion Wiesmann
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Andrew P Weng
- Department of Pathology, British Columbia Cancer Research Center, Vancouver V5Z 1H8, Canada
| | - Jens U Wuerthner
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - David A Williams
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Bruce M Wollison
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Monica M Bertagnolli
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Margaret A Shipp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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