1
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Fay CJ, Iriarte C, Moslehi D, Lam J, Katsyv I, LeBoeuf NR. Ulcerating necrobiotic xanthogranuloma: A clinical sign to reconsider progression from MGUS to multiple myeloma. JAAD Case Rep 2023; 40:1-3. [PMID: 37663892 PMCID: PMC10470407 DOI: 10.1016/j.jdcr.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Affiliation(s)
- Christopher J. Fay
- Department of Dermatology, Brigham and Women's Hospital, Center for Cutaneous Oncology, Dana-Farber/Brigham Cancer Center, Boston, Massachusetts
| | - Christopher Iriarte
- Department of Dermatology, Brigham and Women's Hospital, Center for Cutaneous Oncology, Dana-Farber/Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Dorsa Moslehi
- Department of Dermatology, Brigham and Women's Hospital, Center for Cutaneous Oncology, Dana-Farber/Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jimmy Lam
- Department of Dermatology, Brigham and Women's Hospital, Center for Cutaneous Oncology, Dana-Farber/Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Igor Katsyv
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Nicole R. LeBoeuf
- Department of Dermatology, Brigham and Women's Hospital, Center for Cutaneous Oncology, Dana-Farber/Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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2
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Neff RA, Bosch-Gutierrez A, Sun Y, Katsyv I, Song WM, Wang M, Walsh MJ, Zhang B. Dysfunction of ubiquitin protein ligase MYCBP2 leads to cell resilience in human breast cancers. NAR Cancer 2023; 5:zcad036. [PMID: 37435531 PMCID: PMC10331931 DOI: 10.1093/narcan/zcad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
Breast cancer is the most common type of cancer among women worldwide, and it is estimated that 294 000 new diagnoses and 37 000 deaths will occur each year in the United States alone by 2030. Large-scale genomic studies have identified a number of genetic loci with alterations in breast cancer. However, identification of the genes that are critical for tumorgenicity still remains a challenge. Here, we perform a comprehensive functional multi-omics analysis of somatic mutations in breast cancer and identify previously unknown key regulators of breast cancer tumorgenicity. We identify dysregulation of MYCBP2, an E3 ubiquitin ligase and an upstream regulator of mTOR signaling, is accompanied with decreased disease-free survival. We validate MYCBP2 as a key target through depletion siRNA using in vitro apoptosis assays in MCF10A, MCF7 and T47D cells. We demonstrate that MYCBP2 loss is associated with resistance to apoptosis from cisplatin-induced DNA damage and cell cycle changes, and that CHEK1 inhibition can modulate MYCBP2 activity and caspase cleavage. Furthermore, we show that MYCBP2 knockdown is associated with transcriptomic responses in TSC2 and in apoptosis genes and interleukins. Therefore, we show that MYCBP2 is an important genetic target that represents a key node regulating multiple molecular pathways in breast cancer corresponding with apparent drug resistance in our study.
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Affiliation(s)
- Ryan A Neff
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Almudena Bosch-Gutierrez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yifei Sun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Igor Katsyv
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Martin J Walsh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Mount Sinai Center for RNA Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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3
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Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Tsai EJ, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B. Author Correction: A molecular single-cell lung atlas of lethal COVID-19. Nature 2021; 598:E2. [PMID: 34625743 PMCID: PMC8498978 DOI: 10.1038/s41586-021-03921-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Johannes C Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Huachao Huang
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ajay Nair
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - André F Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chris J Frangieh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA, USA
| | - Aveline Filliol
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Yinshan Fang
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Mariano G Clausi
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - George A Alba
- Department of Medicine, Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean W Chen
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Daniel T Montoro
- Cell Circuits, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Adam E Kornberg
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Arnold S Han
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mathieu F Bakhoum
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA
| | - Niroshana Anandasabapathy
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Dermatology, Weill Cornell Medical College, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xinzheng V Guo
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - Jay H Lefkowitch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Marboe
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Stephen M Lagana
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Emily J Tsai
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Emmanuel Zorn
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Glen S Markowitz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert F Schwabe
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jianwen Que
- Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, USA.
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Program for Mathematical Genomics, Columbia University, New York, NY, USA.
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4
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Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LTY, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CB, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 2021; 595:107-113. [PMID: 33915569 PMCID: PMC8919505 DOI: 10.1038/s41586-021-03570-8] [Citation(s) in RCA: 427] [Impact Index Per Article: 142.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 02/02/2023]
Abstract
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1-4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.
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Affiliation(s)
- Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Carly G. K. Ziegler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA
| | - Graham Heimberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Rachelly Normand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Harvard Medical School, Boston, MA 02115, USA,Massachusetts Institute of Technology, Cambridge, MA
02139, USA
| | - Yiming Yang
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Domenic Abbondanza
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Stephen J. Fleming
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Ayshwarya Subramanian
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Karthik A. Jagadeesh
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Kushal K. Dey
- Department of Epidemiology, Harvard School of Public
Health
| | - Pritha Sen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Division of Infectious Diseases, Department of Medicine,
Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Yered H. Pita-Juárez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Devan Phillips
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Zohar Bloom-Ackermann
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nick Barkas
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki,
Finland,Analytical & Translational Genetics Unit,
Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Gomez
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Johannes C. Melms
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA
| | - Pourya Naderi
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA
| | - Yury V. Popov
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Siddharth S. Raju
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Systems Biology, Harvard Medical School,
Boston, MA 02115, USA,FAS Center for Systems Biology, Department of Organismic
and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian Niezen
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Linus T.-Y. Tsai
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Katherine J. Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA
| | - Malika Sud
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Victoria M. Tran
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shamsudheen K. Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY
| | - Liat Amir-Zilberstein
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Deepak S. Atri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | | | - Olga R. Brook
- Department of Radiology, Beth Israel Deaconess Medical
Center, Boston, MA 02215, USA
| | - Jonathan Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | | | - Phylicia Dorceus
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jesse M. Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Genetics and BASE Initiative, Stanford
University School of Medicine
| | - Adam Essene
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Donna M. Fitzgerald
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robin Fropf
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Joshua Gould
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - John Grzyb
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Tyler Harvey
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Jonathan Hecht
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Tyler Hether
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Hui Ma
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Daniel E. McLoughlin
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Helsinki,
Finland
| | - Robert Padera
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115,Harvard-MIT Division of Health Sciences and Technology,
Cambridge MA,Department of Pathology, Harvard Medical School, Boston,
MA 02115, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Deepti Pant
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Endocrinology, Diabetes, and Metabolism, Beth
Israel Deaconess Medical Center, Boston, MA 02115,Boston Nutrition and Obesity Research Center Functional
Genomics and Bioinformatics Core Boston, MA 02115, USA
| | - Carmel Pe’er
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | | | - Christopher J. Pinto
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacob Plaisted
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Jason Reeves
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Marty Ross
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Melissa Rudy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | | | | | - Alexander Sturm
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, MA, USA,Center for Regenerative Medicine, Massachusetts General
Hospital, Boston, MA 02114, USA
| | - Sarah Warren
- NanoString Technologies Inc., Seattle, WA 98109,
USA
| | - Shuting Zhang
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Lisa Cosimi
- Infectious Diseases Division, Department of Medicine,
Brigham and Women’s Hospital, Boston, MA, USA
| | - Rajat M. Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Divisions of Cardiovascular Medicine and Genetics,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115,
USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia
University Irving Medical Center, New York, NY
| | - Winston Hide
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public
Health
| | - Jayaraj Rajagopal
- Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Stefan Riedel
- Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Gyongyi Szabo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA
| | - Timothy L. Tickle
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of
MIT and Harvard, Cambridge, MA
| | - Deborah Hung
- Infectious Disease and Microbiome Program, Broad
Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston,
MA 02115, USA,Department of Molecular Biology and Center for
Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
02114, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Department of Organismic and Evolutionary Biology,
Harvard University, Cambridge, MA, USA,Department of Immunology and Infectious Diseases, Harvard
T.H. Chan School of Public Health, Harvard University, Boston, MA, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Massachusetts Consortium on Pathogen Readiness, Boston,
MA, USA
| | - Richard Novak
- Wyss Institute for Biologically Inspired Engineering,
Harvard University
| | - Robert Rogers
- Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Massachusetts General Hospital, MA 02114, USA
| | - Donald E. Ingber
- John A. Paulson School of Engineering and Applied
Sciences, Harvard University, Cambridge, MA 02138,Wyss Institute for Biologically Inspired Engineering,
Harvard University,Vascular Biology Program and Department of Surgery,
Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Z. Gordon Jiang
- Harvard Medical School, Boston, MA 02115, USA,Department of Medicine, Beth Israel Deaconess Medical
Center, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition,
Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215,
USA
| | - Dejan Juric
- Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA,Massachusetts General Hospital Cancer Center, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mehrtash Babadi
- Data Sciences Platform, Broad Institute of MIT and
Harvard, Cambridge, MA 02142,Precision Cardiology Laboratory, Broad Institute of MIT
and Harvard, Cambridge, MA 02142, USA
| | - Samouil L. Farhi
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology,
Columbia University Irving Medical Center, New York, NY,Columbia Center for Translational Immunology, New York,
NY,Herbert Irving Comprehensive Cancer Center, Columbia
University Irving Medical Center, New York, NY,Program for Mathematical Genomics, Columbia University
Irving Medical Center, New York, NY
| | - James R. Stone
- Department of Pathology, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02115, USA
| | - Ioannis S. Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA,Harvard Medical School Initiative for RNA Medicine,
Boston, MA 02115, USA,Cancer Research Institute, Beth Israel Deaconess Medical
Center, Boston, MA 02115, USA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s
Hospital, Boston, MA 02115
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Caroline B.M. Porter
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Program in Health Sciences & Technology, Harvard
Medical School & Massachusetts Institute of Technology, Boston, MA 02115,
USA,Institute for Medical Engineering & Science,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
02139, USA,Harvard Graduate Program in Biophysics, Harvard University,
Cambridge, MA 02138, USA,Harvard Medical School, Boston, MA 02115, USA,Harvard Stem Cell Institute, Cambridge, MA, USA,Program in Computational & Systems Biology,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Program in Immunology, Harvard Medical School, Boston, MA
02115, USA,Department of Chemistry, Massachusetts Institute of
Technology, Cambridge, MA 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142,
USA,Center for Immunology and Inflammatory Diseases, Department
of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Center for Cancer Research, Massachusetts General Hospital,
Harvard Medical School, Boston, MA 02114, USA,Department of Medicine, Harvard Medical School, Boston,
MA 02115, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and
Harvard, Cambridge, MA 02142, USA, USA,Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, MA 02139, USA,Howard Hughes Medical Institute, Chevy Chase, MD,
USA,Current address: Genentech, 1 DNA Way, South San
Francisco, CA, USA
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5
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Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B. A molecular single-cell lung atlas of lethal COVID-19. Nature 2021; 595:114-119. [PMID: 33915568 PMCID: PMC8814825 DOI: 10.1038/s41586-021-03569-1] [Citation(s) in RCA: 324] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/19/2021] [Indexed: 01/21/2023]
Abstract
Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection1,2, but the host response at the lung tissue level is poorly understood. Here we performed single-nucleus RNA sequencing of about 116,000 nuclei from the lungs of nineteen individuals who died of COVID-19 and underwent rapid autopsy and seven control individuals. Integrated analyses identified substantial alterations in cellular composition, transcriptional cell states, and cell-to-cell interactions, thereby providing insight into the biology of lethal COVID-19. The lungs from individuals with COVID-19 were highly inflamed, with dense infiltration of aberrantly activated monocyte-derived macrophages and alveolar macrophages, but had impaired T cell responses. Monocyte/macrophage-derived interleukin-1β and epithelial cell-derived interleukin-6 were unique features of SARS-CoV-2 infection compared to other viral and bacterial causes of pneumonia. Alveolar type 2 cells adopted an inflammation-associated transient progenitor cell state and failed to undergo full transition into alveolar type 1 cells, resulting in impaired lung regeneration. Furthermore, we identified expansion of recently described CTHRC1+ pathological fibroblasts3 contributing to rapidly ensuing pulmonary fibrosis in COVID-19. Inference of protein activity and ligand-receptor interactions identified putative drug targets to disrupt deleterious circuits. This atlas enables the dissection of lethal COVID-19, may inform our understanding of long-term complications of COVID-19 survivors, and provides an important resource for therapeutic development.
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Affiliation(s)
- Johannes C. Melms
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Jana Biermann
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Huachao Huang
- Columbia Center for Human Development, New York, NY, USA,Division of Digestive and Liver Diseases, New York, NY, USA,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Yiping Wang
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Ajay Nair
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - André F. Rendeiro
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,These authors contributed equally: Johannes C. Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F. Rendeiro, Amit Dipak Amin
| | - Denis Schapiro
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chris J. Frangieh
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Adrienne M. Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA, USA
| | - Aveline Filliol
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Yinshan Fang
- Columbia Center for Human Development, New York, NY, USA,Division of Digestive and Liver Diseases, New York, NY, USA,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Hiranmayi Ravichandran
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Mariano G. Clausi
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - George A. Alba
- Department of Medicine, Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA
| | - Sean W. Chen
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA
| | - Patricia Ho
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA
| | - Daniel T. Montoro
- Cell Circuits, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Arnold S. Han
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Mathieu F. Bakhoum
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA
| | - Niroshana Anandasabapathy
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Dermatology, Weill Cornell Medical College, New York, NY, USA,Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel F. Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xinzheng V. Guo
- Human Immune Monitoring Core, Columbia University Irving Medical Center, New York, NY, USA
| | - Jay H. Lefkowitch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Charles Marboe
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Stephen M. Lagana
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Emmanuel Zorn
- Columbia Center for Translational Immunology, New York, NY, USA
| | - Glen S. Markowitz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert F. Schwabe
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Robert E. Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar
| | - Jianwen Que
- Columbia Center for Human Development, New York, NY, USA,Division of Digestive and Liver Diseases, New York, NY, USA,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA,Herbert Irving Comprehensive Cancer Center, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar.,,
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA,Columbia Center for Translational Immunology, New York, NY, USA,Herbert Irving Comprehensive Cancer Center, New York, NY, USA,Program for Mathematical Genomics, Columbia University, New York, NY, USA,These authors jointly supervised this work: Robert E. Schwartz, Olivier Elemento, Anjali Saqi, Hanina Hibshoosh, Jianwen Que, Benjamin Izar.,,
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6
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Huang Y, Tejero R, Lee VK, Brusco C, Hannah T, Bertucci TB, Junqueira Alves C, Katsyv I, Kluge M, Foty R, Zhang B, Friedel CC, Dai G, Zou H, Friedel RH. Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics. Commun Biol 2021; 4:145. [PMID: 33514835 PMCID: PMC7846610 DOI: 10.1038/s42003-021-01667-4] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Infiltrative growth is a major cause of high lethality of malignant brain tumors such as glioblastoma (GBM). We show here that GBM cells upregulate guidance receptor Plexin-B2 to gain invasiveness. Deletion of Plexin-B2 in GBM stem cells limited tumor spread and shifted invasion paths from axon fiber tracts to perivascular routes. On a cellular level, Plexin-B2 adjusts cell adhesiveness, migratory responses to different matrix stiffness, and actomyosin dynamics, thus empowering GBM cells to leave stiff tumor bulk and infiltrate softer brain parenchyma. Correspondingly, gene signatures affected by Plexin-B2 were associated with locomotor regulation, matrix interactions, and cellular biomechanics. On a molecular level, the intracellular Ras-GAP domain contributed to Plexin-B2 function, while the signaling relationship with downstream effectors Rap1/2 appeared variable between GBM stem cell lines, reflecting intertumoral heterogeneity. Our studies establish Plexin-B2 as a modulator of cell biomechanics that is usurped by GBM cells to gain invasiveness.
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Affiliation(s)
- Yong Huang
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rut Tejero
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vivian K Lee
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Concetta Brusco
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Theodore Hannah
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Taylor B Bertucci
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Chrystian Junqueira Alves
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ramsey Foty
- Department of Surgery, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Guohao Dai
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Hongyan Zou
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Roland H Friedel
- Friedman Brain Institute, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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7
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Debelenko L, Katsyv I, Chong AM, Peruyero L, Szabolcs M, Uhlemann AC. Trophoblast damage with acute and chronic intervillositis: disruption of the placental barrier by severe acute respiratory syndrome coronavirus 2. Hum Pathol 2020; 109:69-79. [PMID: 33321162 PMCID: PMC7733682 DOI: 10.1016/j.humpath.2020.12.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/18/2020] [Accepted: 12/09/2020] [Indexed: 10/28/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was demonstrated in the placenta; however, the data on the prevalence of placental infection and associated histopathology are limited. To identify the frequency and features of SARS-CoV-2 involvement, we performed a clinicopathologic analysis of 75 placental cases from women infected at the time of delivery and 75 uninfected controls. Placental samples were studied with anti-SARS-CoV-2 immunohistochemistry and/or in situ hybridization. Positive results were confirmed by electron microscopy and quantitative reverse-transcription polymerase chain reaction (qRT-PCR). During delivery, only one woman had symptoms of coronavirus disease 2019, six women reported previous symptoms, and 68 women were asymptomatic. All neonates tested negative for SARS-CoV-2 as per nasopharyngeal swab PCR results. Obstetric histories were unremarkable in 29 of 75 SARS-CoV-2-positive and 8 of 75 SARS-CoV-2-negative women. Placental examination was normal in 12 of 75 infected and 3 of 75 uninfected subjects, respectively. In the remaining cases, placental pathology correlated with obstetric comorbidities without significant differences between SARS-CoV-2-positive and SARS-CoV-2-negative women. SARS-CoV-2 was identified in one placenta of an infected, but asymptomatic, parturient. Viral staining was predominantly localized to the syncytiotrophoblast (STB) which demonstrated marked damage accompanied by perivillous fibrin deposition and mixed intervillositis. A significant decrease of viral titers was detected in the attached umbilical cord compared with the villous parenchyma as per qRT-PCR. SARS-CoV-2 is seldom identified in placentas of infected women. Placental involvement by the virus is characterized by STB damage disrupting the placental barrier and can be seen in asymptomatic mothers without evidence of vertical transmission.
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Affiliation(s)
- Larisa Debelenko
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Igor Katsyv
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Alexander M Chong
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Leonore Peruyero
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matthias Szabolcs
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, 10032, USA
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8
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De Michele S, Sun Y, Yilmaz MM, Katsyv I, Salvatore M, Dzierba AL, Marboe CC, Brodie D, Patel NM, Garcia CK, Saqi A. Forty Postmortem Examinations in COVID-19 Patients. Am J Clin Pathol 2020; 154:748-760. [PMID: 32876680 PMCID: PMC7499554 DOI: 10.1093/ajcp/aqaa156] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Although diffuse alveolar damage, a subtype of acute lung injury (ALI), is the most common microscopic pattern in coronavirus disease 2019 (COVID-19), other pathologic patterns have been described. The aim of the study was to review autopsies from COVID-19 decedents to evaluate the spectrum of pathology and correlate the results with clinical, laboratory, and radiologic findings. METHODS A comprehensive and quantitative review from 40 postmortem examinations was performed. The microscopic patterns were categorized as follows: "major" when present in more than 50% of cases and "novel" if rarely or not previously described and unexpected clinically. RESULTS Three major pulmonary patterns were identified: ALI in 29 (73%) of 40, intravascular fibrin or platelet-rich aggregates (IFPAs) in 36 (90%) of 40, and vascular congestion and hemangiomatosis-like change (VCHL) in 20 (50%) of 40. The absence of ALI (non-ALI) was novel and seen in 11 (27%) of 40. Compared with ALI decedents, those with non-ALI had a shorter hospitalization course (P = .02), chest radiographs with no or minimal consolidation (P = .01), and no pathologically confirmed cause of death (9/11). All non-ALI had VCHL and IFPAs, and clinically most had cardiac arrest. CONCLUSIONS Two distinct pulmonary phenotypic patterns-ALI and non-ALI-were noted. Non-ALI represents a rarely described phenotype. The cause of death in non-ALI is most likely COVID-19 related but requires additional corroboration.
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Affiliation(s)
| | - Yu Sun
- Department of Pathology and Cell Biology
| | | | | | | | | | | | - Daniel Brodie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center and the NewYork-Presbyterian Hospital, New York, NY
| | - Nina M Patel
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center and the NewYork-Presbyterian Hospital, New York, NY
| | - Christine K Garcia
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center and the NewYork-Presbyterian Hospital, New York, NY
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9
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Tejero R, Huang Y, Katsyv I, Kluge M, Lin JY, Tome-Garcia J, Daviaud N, Wang Y, Zhang B, Tsankova NM, Friedel CC, Zou H, Friedel RH. Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment. EBioMedicine 2019; 42:252-269. [PMID: 30952620 PMCID: PMC6491796 DOI: 10.1016/j.ebiom.2019.03.064] [Citation(s) in RCA: 65] [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: 07/27/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 12/18/2022] Open
Abstract
Background Glioblastoma (GBM), a highly malignant brain tumor, invariably recurs after therapy. Quiescent GBM cells represent a potential source of tumor recurrence, but little is known about their molecular underpinnings. Methods Patient-derived GBM cells were engineered by CRISPR/Cas9-assisted knock-in of an inducible histone2B-GFP (iH2B-GFP) reporter to track cell division history. We utilized an in vitro 3D GBM organoid approach to isolate live quiescent GBM (qGBM) cells and their proliferative counterparts (pGBM) to compare stem cell properties and therapy resistance. Gene expression programs of qGBM and pGBM cells were analyzed by RNA-Seq and NanoString platforms. Findings H2B-GFP-retaining qGBM cells exhibited comparable self-renewal capacity but higher therapy resistance relative to pGBM. Quiescent GBM cells expressed distinct gene programs that affect cell cycle control, metabolic adaptation, and extracellular matrix (ECM) interactions. Transcriptome analysis also revealed a mesenchymal shift in qGBM cells of both proneural and mesenchymal GBM subtypes. Bioinformatic analyses and functional assays in GBM organoids established hypoxia and TGFβ signaling as potential niche factors that promote quiescence in GBM. Finally, network co-expression analysis of TCGA glioma patient data identified gene modules that are enriched for qGBM signatures and also associated with survival rate. Interpretation Our in vitro study in 3D GBM organoids supports the presence of a quiescent cell population that displays self-renewal capacity, high therapy resistance, and mesenchymal gene signatures. It also sheds light on how GBM cells may acquire and maintain quiescence through ECM organization and interaction with niche factors such as TGFβ and hypoxia. Our findings provide a starting point for developing strategies to tackle the quiescent population of GBM. Fund National Institutes of Health (NIH) and Deutsche Forschungsgemeinschaft (DFG).
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Affiliation(s)
- Rut Tejero
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yong Huang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jung-Yi Lin
- Tisch Cancer Institute, Biostatistics Shared Resource Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Tome-Garcia
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas Daviaud
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuanshuo Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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10
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Tome-Garcia J, Erfani P, Nudelman G, Tsankov AM, Katsyv I, Tejero R, Bin Zhang, Walsh M, Friedel RH, Zaslavsky E, Tsankova NM. Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma. Nat Commun 2018; 9:4020. [PMID: 30275445 PMCID: PMC6167382 DOI: 10.1038/s41467-018-06258-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 08/21/2018] [Indexed: 12/17/2022] Open
Abstract
The intrinsic drivers of migration in glioblastoma (GBM) are poorly understood. To better capture the native molecular imprint of GBM and its developmental context, here we isolate human stem cell populations from GBM (GSC) and germinal matrix tissues and map their chromatin accessibility via ATAC-seq. We uncover two distinct regulatory GSC signatures, a developmentally shared/proliferative and a tumor-specific/migratory one in which TEAD1/4 motifs are uniquely overrepresented. Using ChIP-PCR, we validate TEAD1 trans occupancy at accessibility sites within AQP4, EGFR, and CDH4. To further characterize TEAD’s functional role in GBM, we knockout TEAD1 or TEAD4 in patient-derived GBM lines using CRISPR-Cas9. TEAD1 ablation robustly diminishes migration, both in vitro and in vivo, and alters migratory and EMT transcriptome signatures with consistent downregulation of its target AQP4. TEAD1 overexpression restores AQP4 expression, and both TEAD1 and AQP4 overexpression rescue migratory deficits in TEAD1-knockout cells, implicating a direct regulatory role for TEAD1–AQP4 in GBM migration. The intrinsic drivers of glioblastoma (GBM) migration are still poorly understood. Here the authors purify GBM stem cells (GSCs) from patients and profile chromatin accessibility in these cells, identifying TEAD1 as a regulator of migration in human glioblastoma.
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Affiliation(s)
- Jessica Tome-Garcia
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Parsa Erfani
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Igor Katsyv
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rut Tejero
- Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Martin Walsh
- Department of Pharmacological Sciences, Center for RNA Biology and Medicine, New York, NY, 10029, USA
| | - Roland H Friedel
- Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Neuroscience and The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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11
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Zhou X, Wang M, Katsyv I, Irie H, Zhang B. EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy. Bioinformatics 2018; 34:3151-3159. [PMID: 29688306 PMCID: PMC6138000 DOI: 10.1093/bioinformatics/bty325] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 04/20/2018] [Indexed: 01/31/2023] Open
Abstract
Motivation Availability of large-scale genomic, epigenetic and proteomic data in complex diseases makes it possible to objectively and comprehensively identify the therapeutic targets that can lead to new therapies. The Connectivity Map has been widely used to explore novel indications of existing drugs. However, the prediction accuracy of the existing methods, such as Kolmogorov-Smirnov statistic remains low. Here we present a novel high-performance drug repositioning approach that improves over the state-of-the-art methods. Results We first designed an expression weighted cosine (EWCos) method to minimize the influence of the uninformative expression changes and then developed an ensemble approach termed ensemble of multiple drug repositioning approaches (EMUDRA) to integrate EWCos and three existing state-of-the-art methods. EMUDRA significantly outperformed individual drug repositioning methods when applied to simulated and independent evaluation datasets. We predicted using EMUDRA and experimentally validated an antibiotic rifabutin as an inhibitor of cell growth in triple negative breast cancer. EMUDRA can identify drugs that more effectively target disease gene signatures and will thus be a useful tool for identifying novel therapies for complex diseases and predicting new indications for existing drugs. Availability and implementation The EMUDRA R package is available at doi: 10.7303/syn11510888. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hanna Irie
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- To whom correspondence should be addressed. ,
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12
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Katsyv I, Wang M, Song WM, Zhou X, Zhao Y, Park S, Zhu J, Zhang B, Irie HY. EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer. Oncotarget 2018; 7:69592-69605. [PMID: 27612429 PMCID: PMC5342500 DOI: 10.18632/oncotarget.11870] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 05/04/2016] [Accepted: 08/25/2016] [Indexed: 02/06/2023] Open
Abstract
Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation. Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases. Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has identified any underlying mechanism about how EPRS contributes to carcinogenesis. In this study, we identified EPRS as upregulated in estrogen receptor positive (ER+) human breast tumors in the TCGA and METABRIC cohorts, with copy number gains in nearly 50% of samples in both datasets. EPRS expression is associated with reduced overall survival in patients with ER+ tumors in TCGA and METABRIC datasets. EPRS expression was also associated with reduced distant relapse-free survival in patients treated with adjuvant tamoxifen monotherapy for five years, and EPRS-correlated genes were highly enriched for genes predictive of a poor response to tamoxifen. We demonstrated the necessity of EPRS for proliferation of tamoxifen-resistant ER+ breast cancer, but not ER- breast cancer cells. Transcriptomic profiling showed that EPRS regulated cell cycle and estrogen response genes. Finally, we constructed a causal gene network based on over 2500 ER+ breast tumor samples to build up an EPRS-estrogen signaling pathway. EPRS and its regulated estrogenic gene network may offer a promising alternative approach to target ER+ breast cancers that are refractory to current anti-estrogens.
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Affiliation(s)
- Igor Katsyv
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Won Min Song
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianxiao Zhou
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongzhong Zhao
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sun Park
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jun Zhu
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanna Y Irie
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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13
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Ito K, Park SH, Katsyv I, Zhang W, De Angelis C, Schiff R, Irie HY. PTK6 regulates growth and survival of endocrine therapy-resistant ER+ breast cancer cells. NPJ Breast Cancer 2017; 3:45. [PMID: 29167821 PMCID: PMC5694002 DOI: 10.1038/s41523-017-0047-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 09/25/2017] [Accepted: 10/19/2017] [Indexed: 12/14/2022] Open
Abstract
The non-receptor tyrosine kinase, PTK6/BRK, is highly expressed in multiple tumor types, including prostate, ovarian, and breast cancers, and regulates oncogenic phenotypes such as proliferation, migration, and survival. PTK6 inhibition also overcomes targeted therapy resistance of HER2+ breast cancer. Although PTK6 is highly expressed in ER+ Luminal breast cancers, the role of PTK6 in this subtype has not been elucidated. In this study, we investigated the functions of PTK6 in ER+ Luminal breast cancer cells, including those that are relatively resistant to estrogen deprivation or targeted endocrine therapies used in the treatment of ER+ cancers. Enhanced expression of PTK6 in ER+ breast cancer cells enhances growth of ER+ breast cancer cells, including tamoxifen-treated cells. Downregulation of PTK6 in ER+ breast cancer cells, including those resistant to tamoxifen, fulvestrant, and estrogen deprivation, induces apoptosis, as evidenced by increased levels of cleaved PARP, and an increase in the AnnexinV+ population. PTK6 downregulation impairs growth of these cells in 3D MatrigelTM cultures, and virtually abrogates primary tumor growth of both tamoxifen-sensitive and resistant MCF-7 xenografts. Finally, we show that p38 MAPK activation is critical for PTK6 downregulation-induced apoptosis, a mechanism that we previously reported for survival of HER2+ breast cancer cells, highlighting conserved mechanisms of survival regulation by PTK6 across breast cancer subtypes. In conclusion, our studies elucidate critical functions of PTK6 in ER+ Luminal breast cancers and support PTK6 as an attractive therapeutic target for ER+ breast cancers. Drugs that target a tumor-promoting enzyme called protein tyrosine kinase 6 (PTK6) could help treat hormone-receptor positive breast cancer. A team led by Hanna Irie from the Icahn School of Medicine at Mount Sinai in New York, NY, USA, investigated the role of PTK6, also known as breast tumor kinase, in breast cancer cells that grow in response to the hormone estrogen. They boosted the enzyme’s expression in estrogen receptor-expressing breast cancer cells and saw enhanced growth. Conversely, downregulating PTK6 levels led to cell death, including in tumor cells that were resistant to tamoxifen
and other therapies commonly used to treat estrogen-receptor positive breast cancer. The researchers showed that this effect was dependent on the activation of a signaling pathway previously found to be important in another subtype of breast cancer, highlighting a conserved mechanism of cell survival regulation by PTK6.
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Affiliation(s)
- Koichi Ito
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY USA
| | - Sun Hee Park
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Carmine De Angelis
- Lester & Sue Smith Breast Center, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX USA.,Department of Medicine, Baylor College of Medicine, Houston, TX USA
| | - Rachel Schiff
- Lester & Sue Smith Breast Center, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX USA.,Department of Medicine, Baylor College of Medicine, Houston, TX USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Hanna Y Irie
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY USA.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY USA
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14
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McKenzie AT, Moyon S, Wang M, Katsyv I, Song WM, Zhou X, Dammer EB, Duong DM, Aaker J, Zhao Y, Beckmann N, Wang P, Zhu J, Lah JJ, Seyfried NT, Levey AI, Katsel P, Haroutunian V, Schadt EE, Popko B, Casaccia P, Zhang B. Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer's disease. Mol Neurodegener 2017; 12:82. [PMID: 29110684 PMCID: PMC5674813 DOI: 10.1186/s13024-017-0219-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/17/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Oligodendrocytes (OLs) and myelin are critical for normal brain function and have been implicated in neurodegeneration. Several lines of evidence including neuroimaging and neuropathological data suggest that Alzheimer's disease (AD) may be associated with dysmyelination and a breakdown of OL-axon communication. METHODS In order to understand this phenomenon on a molecular level, we systematically interrogated OL-enriched gene networks constructed from large-scale genomic, transcriptomic and proteomic data obtained from human AD postmortem brain samples. We then validated these networks using gene expression datasets generated from mice with ablation of major gene expression nodes identified in our AD-dysregulated networks. RESULTS The robust OL gene coexpression networks that we identified were highly enriched for genes associated with AD risk variants, such as BIN1 and demonstrated strong dysregulation in AD. We further corroborated the structure of the corresponding gene causal networks using datasets generated from the brain of mice with ablation of key network drivers, such as UGT8, CNP and PLP1, which were identified from human AD brain data. Further, we found that mice with genetic ablations of Cnp mimicked aspects of myelin and mitochondrial gene expression dysregulation seen in brain samples from patients with AD, including decreased protein expression of BIN1 and GOT2. CONCLUSIONS This study provides a molecular blueprint of the dysregulation of gene expression networks of OL in AD and identifies key OL- and myelination-related genes and networks that are highly associated with AD.
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Affiliation(s)
- Andrew T. McKenzie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Sarah Moyon
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Neuroscience Initiative, The City University of New York, Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY 10031 USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Eric B. Dammer
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Joshua Aaker
- Department of Neurology, The University of Chicago Pritzker School of Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637 USA
| | - Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Noam Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 USA
- Integrated Proteomics Core Facility, Emory University School of Medicine, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Allan I. Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322 USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Pavel Katsel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Vahram Haroutunian
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY 10468 USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Brian Popko
- Department of Neurology, The University of Chicago Pritzker School of Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637 USA
| | - Patrizia Casaccia
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
- Neuroscience Initiative, The City University of New York, Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY 10031 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
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15
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Irie HY, Park SH, Katsyv I, Zhang W, Nayak A. Abstract P3-04-13: Protein tyrosine kinase 6 (PTK6) promotes survival of endocrine therapy-resistant ER+ breast cancer cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p3-04-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background/Rationale: The non-receptor tyrosine kinase PTK6/Brk is highly expressed in the ER+/Luminal breast cancer subtypes. PTK6 expression has prognostic significance for patients with ER+ disease; higher transcript levels are associated with poorer survival. The functions of PTK6 in the context of ER+ breast cancer and sensitivity to endocrine therapy have not been explored. We sought to determine the functional roles of PTK6 in ER+ breast cancer cells, including those that are relatively resistant to current endocrine therapies. Methods/Results. We modulated the expression of PTK6 using both gain- and loss-of-function approaches. Enhanced expression of PTK6 in Tamoxifen-sensitive ER+ breast cancer cells was sufficient to confer relative Tamoxifen resistance. Furthermore, downregulation of PTK6 in ER+ breast cancer cells, including those that have acquired resistance to Tamoxifen, induced apoptosis, as evidenced by an increase in AnnexinV+ cells and increased levels of cleaved PARP. PTK6 downregulation impaired growth of Tamoxifen-resistant variants of ER+ MCF7 and T47D cells (MCF7TamR and T47DTamR) in 3D Matrigel culture, and virtually abrogated primary tumor growth of MCF7TamR xenografts. Mechanistically, p38MAPK activation is critical for PTK6 downregulation-induced apoptosis of ER+ breast cancer cells, as p38 inhibition partially rescues cells from PTK6 shRNA-associated apoptosis. Conclusions: Our studies highlight the critical role that PTK6 plays in the survival of ER+ breast cancer cells, including those that are resistant to endocrine therapy. Enhanced PTK6 expression in ER+ breast cancer cells is sufficient to promote endocrine therapy resistance, which could contribute to the poorer prognosis associated with higher PTK6 expression in ER+ patient tumors. As small molecule PTK6 inhibitors are becoming available, our studies support further evaluation of PTK6 as a candidate therapeutic target for endocrine therapy resistant ER+ breast cancers.
Citation Format: Irie HY, Park SH, Katsyv I, Zhang W, Nayak A. Protein tyrosine kinase 6 (PTK6) promotes survival of endocrine therapy-resistant ER+ breast cancer cells [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-04-13.
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Affiliation(s)
- HY Irie
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - SH Park
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - I Katsyv
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - W Zhang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - A Nayak
- Icahn School of Medicine at Mount Sinai, New York, NY
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16
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McKenzie AT, Katsyv I, Song WM, Wang M, Zhang B. DGCA: A comprehensive R package for Differential Gene Correlation Analysis. BMC Syst Biol 2016; 10:106. [PMID: 27846853 PMCID: PMC5111277 DOI: 10.1186/s12918-016-0349-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/03/2016] [Indexed: 12/31/2022]
Abstract
Background Dissecting the regulatory relationships between genes is a critical step towards building accurate predictive models of biological systems. A powerful approach towards this end is to systematically study the differences in correlation between gene pairs in more than one distinct condition. Results In this study we develop an R package, DGCA (for Differential Gene Correlation Analysis), which offers a suite of tools for computing and analyzing differential correlations between gene pairs across multiple conditions. To minimize parametric assumptions, DGCA computes empirical p-values via permutation testing. To understand differential correlations at a systems level, DGCA performs higher-order analyses such as measuring the average difference in correlation and multiscale clustering analysis of differential correlation networks. Through a simulation study, we show that the straightforward z-score based method that DGCA employs significantly outperforms the existing alternative methods for calculating differential correlation. Application of DGCA to the TCGA RNA-seq data in breast cancer not only identifies key changes in the regulatory relationships between TP53 and PTEN and their target genes in the presence of inactivating mutations, but also reveals an immune-related differential correlation module that is specific to triple negative breast cancer (TNBC). Conclusions DGCA is an R package for systematically assessing the difference in gene-gene regulatory relationships under different conditions. This user-friendly, effective, and comprehensive software tool will greatly facilitate the application of differential correlation analysis in many biological studies and thus will help identification of novel signaling pathways, biomarkers, and targets in complex biological systems and diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0349-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew T McKenzie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA. .,Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY, 10029, USA.
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17
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Byerly J, Halstead-Nussloch G, Ito K, Katsyv I, Irie HY. PRKCQ promotes oncogenic growth and anoikis resistance of a subset of triple-negative breast cancer cells. Breast Cancer Res 2016; 18:95. [PMID: 27663795 PMCID: PMC5034539 DOI: 10.1186/s13058-016-0749-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 01/20/2016] [Accepted: 08/20/2016] [Indexed: 12/02/2022] Open
Abstract
Background The protein kinase C (PKC) family comprises distinct classes of proteins, many of which are implicated in diverse cellular functions. Protein tyrosine kinase C theta isoform (PRKCQ)/PKCθ, a member of the novel PKC family, may have a distinct isoform-specific role in breast cancer. PKCθ is preferentially expressed in triple-negative breast cancer (TNBC) compared to other breast tumor subtypes. We hypothesized that PRKCQ/PKCθ critically regulates growth and survival of a subset of TNBC cells. Methods To elucidate the role of PRKCQ/PKCθ in regulating growth and anoikis resistance, we used both gain and loss of function to modulate expression of PRKCQ. We enhanced expression of PKCθ (kinase-active or inactive) in non-transformed breast epithelial cells (MCF-10A) and assessed effects on epidermal growth factor (EGF)-independent growth, anoikis, and migration. We downregulated expression of PKCθ in TNBC cells, and determined effects on in vitro and in vivo growth and survival. TNBC cells were also treated with a small molecule inhibitor to assess requirement for PKCθ kinase activity in the growth of TNBC cells. Results PRKCQ/PKCθ can promote oncogenic phenotypes when expressed in non-transformed MCF-10A mammary epithelial cells; PRKCQ/PKCθ enhances anchorage-independent survival, growth-factor-independent proliferation, and migration. PKCθ expression promotes retinoblastoma (Rb) phosphorylation and cell-cycle progression under growth factor-deprived conditions that typically induce cell-cycle arrest of MCF-10A breast epithelial cells. Proliferation and Rb phosphorylation are dependent on PKCθ-stimulated extracellular signal-related kinase (Erk)/mitogen-activated protein kinase (MAPK) activity. Enhanced Erk/MAPK activity is dependent on the kinase activity of PKCθ, as overexpression of kinase-inactive PKCθ does not stimulate Erk/MAPK or Rb phosphorylation or promote growth-factor-independent proliferation. Downregulation of PRKCQ/PKCθ in TNBC cells enhances anoikis, inhibits growth in 3-D MatrigelTM cultures, and impairs triple-negative tumor xenograft growth. AEB071, an inhibitor of PKCθ kinase activity, also inhibits growth and invasive branching of TNBC cells in 3-D cultures, further supporting a role for PKCθ kinase activity in triple-negative cancer cell growth. Conclusions Enhanced PRKCQ/PKCθ expression can promote growth-factor-independent growth, anoikis resistance, and migration. PRKCQ critically regulates growth and survival of a subset of TNBC. Inhibition of PKCθ kinase activity may be an attractive therapeutic approach for TNBC, a subtype in need of improved targeted therapies. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0749-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Byerly
- Division of Hematology and Medical Oncology, Department of Medicine and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA
| | - Gwyneth Halstead-Nussloch
- Division of Hematology and Medical Oncology, Department of Medicine and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA
| | - Koichi Ito
- Division of Hematology and Medical Oncology, Department of Medicine and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA
| | - Igor Katsyv
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hanna Y Irie
- Division of Hematology and Medical Oncology, Department of Medicine and Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA. .,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA.
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18
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Zhang B, McKenzie A, Wang M, Katsyv I, Song WM, Zhou X, Popko B, Aaker J, Tredici K, Nave KA, Zhu J, Schadt E, Casaccia P. F2‐01‐01: Oligodendrocyte‐Enriched Gene Networks Reveal Novel Pathways and Key Targets in the Pathogenesis of Alzheimer’s Disease. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Bin Zhang
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | | | - Minghui Wang
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Igor Katsyv
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Won-min Song
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Xianxiao Zhou
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | | | | | | | | | - Jun Zhu
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
| | - Eric Schadt
- Icahn School of Medicine at Mount SinaiNew YorkNY USA
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Park SH, Ito K, Olcott W, Katsyv I, Halstead-Nussloch G, Irie HY. PTK6 inhibition promotes apoptosis of Lapatinib-resistant Her2(+) breast cancer cells by inducing Bim. Breast Cancer Res 2015; 17:86. [PMID: 26084280 PMCID: PMC4496943 DOI: 10.1186/s13058-015-0594-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 06/02/2015] [Indexed: 01/06/2023] Open
Abstract
Introduction Protein tyrosine kinase 6 (PTK6) is a non-receptor tyrosine kinase that is highly expressed in Human Epidermal Growth Factor 2+ (Her2+) breast cancers. Overexpression of PTK6 enhances anchorage-independent survival, proliferation, and migration of breast cancer cells. We hypothesized that PTK6 inhibition is an effective strategy to inhibit growth and survival of Her2+ breast cancer cells, including those that are relatively resistant to Lapatinib, a targeted therapy for Her2+ breast cancer, either intrinsically or acquired after continuous drug exposure. Methods To determine the effects of PTK6 inhibition on Lapatinib-resistant Her2+ breast cancer cell lines (UACC893R1 and MDA-MB-453), we used short hairpin ribonucleic acid (shRNA) vectors to downregulate PTK6 expression. We determined the effects of PTK6 downregulation on growth and survival in vitro and in vivo, as well as the mechanisms responsible for these effects. Results Lapatinib treatment of “sensitive” Her2+ cells induces apoptotic cell death and enhances transcript and protein levels of Bim, a pro-apoptotic Bcl2 family member. In contrast, treatment of relatively “resistant” Her2+ cells fails to induce Bim or enhance levels of cleaved, poly-ADP ribose polymerase (PARP). Downregulation of PTK6 expression in these “resistant” cells enhances Bim expression, resulting in apoptotic cell death. PTK6 downregulation impairs growth of these cells in in vitro 3-D MatrigelTM cultures, and also inhibits growth of Her2+ primary tumor xenografts. Bim expression is critical for apoptosis induced by PTK6 downregulation, as co-expression of Bim shRNA rescued these cells from PTK6 shRNA-induced death. The regulation of Bim by PTK6 is not via changes in Erk/MAPK or Akt signaling, two pathways known to regulate Bim expression. Rather, PTK6 downregulation activates p38, and pharmacological inhibition of p38 activity prevents PTK6 shRNA-induced Bim expression and partially rescues cells from apoptosis. Conclusions PTK6 downregulation induces apoptosis of Lapatinib-resistant Her2+ breast cancer cells by enhancing Bim expression via p38 activation. As Bim expression is a critical biomarker for response to many targeted therapies, PTK6 inhibition may offer a therapeutic approach to treating patients with Her2 targeted therapy-resistant breast cancers. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0594-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sun Hee Park
- Division of Hematology and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA.
| | - Koichi Ito
- Division of Hematology and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA.
| | - William Olcott
- Division of Hematology and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA.
| | - Igor Katsyv
- Division of Hematology and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA.
| | - Gwyneth Halstead-Nussloch
- Division of Hematology and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA.
| | - Hanna Y Irie
- Division of Hematology and Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA. .,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, USA.
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20
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Abstract
Malignant gliomas, which include glioblastomas and anaplastic astrocytomas, are the most common primary tumors of the brain. Over the past 30 years, the standard treatment for these tumors has evolved to include maximal safe surgical resection, radiation therapy and temozolomide chemotherapy. While the median survival of patients with glioblastomas has improved from 6 months to 14.6 months, these tumors continue to be lethal for the vast majority of patients. There has, however, been recent substantial progress in our mechanistic understanding of tumor development and growth. The translation of these genetic, epigenetic and biochemical findings into therapies that have been tested in clinical trials is the subject of this review.
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Affiliation(s)
- Leopold Arko
- Surgical and Molecular Neuro-oncology Unit, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
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