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Amar D, Gay NR, Jean-Beltran PM, Bae D, Dasari S, Dennis C, Evans CR, Gaul DA, Ilkayeva O, Ivanova AA, Kachman MT, Keshishian H, Lanza IR, Lira AC, Muehlbauer MJ, Nair VD, Piehowski PD, Rooney JL, Smith KS, Stowe CL, Zhao B, Clark NM, Jimenez-Morales D, Lindholm ME, Many GM, Sanford JA, Smith GR, Vetr NG, Zhang T, Almagro Armenteros JJ, Avila-Pacheco J, Bararpour N, Ge Y, Hou Z, Marwaha S, Presby DM, Natarajan Raja A, Savage EM, Steep A, Sun Y, Wu S, Zhen J, Bodine SC, Esser KA, Goodyear LJ, Schenk S, Montgomery SB, Fernández FM, Sealfon SC, Snyder MP, Adkins JN, Ashley E, Burant CF, Carr SA, Clish CB, Cutter G, Gerszten RE, Kraus WE, Li JZ, Miller ME, Nair KS, Newgard C, Ortlund EA, Qian WJ, Tracy R, Walsh MJ, Wheeler MT, Dalton KP, Hastie T, Hershman SG, Samdarshi M, Teng C, Tibshirani R, Cornell E, Gagne N, May S, Bouverat B, Leeuwenburgh C, Lu CJ, Pahor M, Hsu FC, Rushing S, Walkup MP, Nicklas B, Rejeski WJ, Williams JP, Xia A, Albertson BG, Barton ER, Booth FW, Caputo T, Cicha M, De Sousa LGO, Farrar R, Hevener AL, Hirshman MF, Jackson BE, Ke BG, Kramer KS, Lessard SJ, Makarewicz NS, Marshall AG, Nigro P, Powers S, Ramachandran K, Rector RS, Richards CZT, Thyfault J, Yan Z, Zang C, Amper MAS, Balci AT, Chavez C, Chikina M, Chiu R, Gritsenko MA, Guevara K, Hansen JR, Hennig KM, Hung CJ, Hutchinson-Bunch C, Jin CA, Liu X, Maner-Smith KM, Mani DR, Marjanovic N, Monroe ME, Moore RJ, Moore SG, Mundorff CC, Nachun D, Nestor MD, Nudelman G, Pearce C, Petyuk VA, Pincas H, Ramos I, Raskind A, Rirak S, Robbins JM, Rubenstein AB, Ruf-Zamojski F, Sagendorf TJ, Seenarine N, Soni T, Uppal K, Vangeti S, Vasoya M, Vornholt A, Yu X, Zaslavsky E, Zebarjadi N, Bamman M, Bergman BC, Bessesen DH, Buford TW, Chambers TL, Coen PM, Cooper D, Haddad F, Gadde K, Goodpaster BH, Harris M, Huffman KM, Jankowski CM, Johannsen NM, Kohrt WM, Lester B, Melanson EL, Moreau KL, Musi N, Newton RL, Radom-Aizik S, Ramaker ME, Rankinen T, Rasmussen BB, Ravussin E, Schauer IE, Schwartz RS, Sparks LM, Thalacker-Mercer A, Trappe S, Trappe TA, Volpi E. Temporal dynamics of the multi-omic response to endurance exercise training. Nature 2024; 629:174-183. [PMID: 38693412 PMCID: PMC11062907 DOI: 10.1038/s41586-023-06877-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/16/2023] [Indexed: 05/03/2024]
Abstract
Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood1-3. Here, the Molecular Transducers of Physical Activity Consortium4 profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository ( https://motrpac-data.org/ ).
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2
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Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat Comput Sci 2023; 3:805. [PMID: 38177788 PMCID: PMC10766523 DOI: 10.1038/s43588-023-00523-1] [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] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Affiliation(s)
- Xi Chen
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yuan Wang
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wan-Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare M Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aliza B Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alicja Tadych
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexandria Vornholt
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Felicia Ruffin
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Michael Dagher
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Daniel G Chawla
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | | | | | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven H Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, USA.
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Chen X, Wang Y, Cappuccio A, Cheng WS, Zamojski FR, Nair VD, Miller CM, Rubenstein AB, Nudelman G, Tadych A, Theesfeld CL, Vornholt A, George MC, Ruffin F, Dagher M, Chawla DG, Soares-Schanoski A, Spurbeck RR, Ndhlovu LC, Sebra R, Kleinstein SH, Letizia AG, Ramos I, Fowler VG, Woods CW, Zaslavsky E, Troyanskaya OG, Sealfon SC. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nat Comput Sci 2023; 3:644-657. [PMID: 37974651 PMCID: PMC10653299 DOI: 10.1038/s43588-023-00476-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/06/2023] [Indexed: 11/19/2023]
Abstract
Resolving chromatin-remodeling-linked gene expression changes at cell-type resolution is important for understanding disease states. Here we describe MAGICAL (Multiome Accessibility Gene Integration Calling and Looping), a hierarchical Bayesian approach that leverages paired single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single-cell data that we generated from subjects with bloodstream infection and uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be activated by bacterial sepsis. We addressed the challenging problem of distinguishing host regulatory circuit responses to methicillin-resistant and methicillin-susceptible S. aureus infections. Although differential expression analysis failed to show predictive value, MAGICAL identified epigenetic circuit biomarkers that distinguished methicillin-resistant from methicillin-susceptible S. aureus infections.
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Affiliation(s)
- Xi Chen
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yuan Wang
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wan-Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aliza B. Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alicja Tadych
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Chandra L. Theesfeld
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexandria Vornholt
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Felicia Ruffin
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Michael Dagher
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Daniel G. Chawla
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | | | | | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven H. Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Christopher W. Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
| | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- These authors jointly supervised this work: Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon
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4
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Wang W, Hariharan M, Bartlett A, Barragan C, Castanon R, Rothenberg V, Song H, Nery J, Aldridge A, Altshul J, Kenworthy M, Ding W, Liu H, Tian W, Zhou J, Chen H, Wei B, Gündüz IB, Norell T, Broderick TJ, McClain MT, Satterwhite LL, Burke TW, Petzold EA, Shen X, Woods CW, Fowler VG, Ruffin F, Panuwet P, Barr DB, Beare JL, Smith AK, Spurbeck RR, Vangeti S, Ramos I, Nudelman G, Sealfon SC, Castellino F, Walley AM, Evans T, Müller F, Greenleaf WJ, Ecker JR. Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures. bioRxiv 2023:2023.06.29.546792. [PMID: 37425926 PMCID: PMC10327221 DOI: 10.1101/2023.06.29.546792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Variations in DNA methylation patterns in human tissues have been linked to various environmental exposures and infections. Here, we identified the DNA methylation signatures associated with multiple exposures in nine major immune cell types derived from peripheral blood mononuclear cells (PBMCs) at single-cell resolution. We performed methylome sequencing on 111,180 immune cells obtained from 112 individuals who were exposed to different viruses, bacteria, or chemicals. Our analysis revealed 790,662 differentially methylated regions (DMRs) associated with these exposures, which are mostly individual CpG sites. Additionally, we integrated methylation and ATAC-seq data from same samples and found strong correlations between the two modalities. However, the epigenomic remodeling in these two modalities are complementary. Finally, we identified the minimum set of DMRs that can predict exposures. Overall, our study provides the first comprehensive dataset of single immune cell methylation profiles, along with unique methylation biomarkers for various biological and chemical exposures.
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Affiliation(s)
- Wenliang Wang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Manoj Hariharan
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Cesar Barragan
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Rosa Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Vince Rothenberg
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Haili Song
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Joseph Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Andrew Aldridge
- Duke University School of Medicine, Bryan Research Building, 311 Research Drive, Durham, NC 27710, USA
| | - Jordan Altshul
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Mia Kenworthy
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Wubin Ding
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Wei Tian
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jingtian Zhou
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Bei Wei
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Irem B. Gündüz
- Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrücken, Germany
| | - Todd Norell
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA
| | - Timothy J Broderick
- Healthspan, Resilience, and Performance, Florida Institute for Human and Machine Cognition, 40 S Alcaniz St, Pensacola, FL 32502, USA
| | - Micah T. McClain
- Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA
- Durham Veterans Affairs Medical Center, Durham, NC 27705 USA
| | - Lisa L. Satterwhite
- Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Thomas W. Burke
- Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA
| | - Elizabeth A. Petzold
- Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA
| | - Xiling Shen
- Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA
| | - Christopher W. Woods
- Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA
- Durham Veterans Affairs Medical Center, Durham, NC 27705 USA
| | - Vance G. Fowler
- Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA
- Duke Clinical Research Institute, Durham NC 27701 USA
| | - Felicia Ruffin
- Center for Infectious Disease Diagnostics and Innovation, Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710 USA
| | - Parinya Panuwet
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
| | - Dana B. Barr
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
| | | | - Anthony K. Smith
- Battelle Memorial Institute, 505 King Ave Columbus OH 43201, USA
| | | | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, 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
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai; New York, NY 10029, USA
| | - Flora Castellino
- U.S. Department of Health and Human Services, Administration for Strategic Preparedness and Response, Biomedical Advanced Research and Development Authority, Washington, DC, USA
| | - Anna Maria Walley
- Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom
| | - Thomas Evans
- Vaccitech plc, Unit 6-10, Zeus Building, Rutherford Avenue, Harwell OX11 0DF, United Kingdom
| | - Fabian Müller
- Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrücken, Germany
| | | | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
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5
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Mao W, Miller CM, Nair VD, Ge Y, Amper MAS, Cappuccio A, George M, Goforth CW, Guevara K, Marjanovic N, Nudelman G, Pincas H, Ramos I, Sealfon RSG, Soares‐Schanoski A, Vangeti S, Vasoya M, Weir DL, Zaslavsky E, Kim‐Schulze S, Gnjatic S, Merad M, Letizia AG, Troyanskaya OG, Sealfon SC, Chikina M. A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation. Mol Syst Biol 2023; 19:e11361. [PMID: 36919946 PMCID: PMC10167476 DOI: 10.15252/msb.202211361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA methylation comprises a cumulative record of lifetime exposures superimposed on genetically determined markers. Little is known about methylation dynamics in humans following an acute perturbation, such as infection. We characterized the temporal trajectory of blood epigenetic remodeling in 133 participants in a prospective study of young adults before, during, and after asymptomatic and mildly symptomatic SARS-CoV-2 infection. The differential methylation caused by asymptomatic or mildly symptomatic infections was indistinguishable. While differential gene expression largely returned to baseline levels after the virus became undetectable, some differentially methylated sites persisted for months of follow-up, with a pattern resembling autoimmune or inflammatory disease. We leveraged these responses to construct methylation-based machine learning models that distinguished samples from pre-, during-, and postinfection time periods, and quantitatively predicted the time since infection. The clinical trajectory in the young adults and in a diverse cohort with more severe outcomes was predicted by the similarity of methylation before or early after SARS-CoV-2 infection to the model-defined postinfection state. Unlike the phenomenon of trained immunity, the postacute SARS-CoV-2 epigenetic landscape we identify is antiprotective.
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Affiliation(s)
- Weiguang Mao
- Department of Computational and Systems Biology, School of MedicineUniversity of PittsburghPAPittsburghUSA
- Present address:
Center for Computational BiologyFlatiron Institute, Simons FoundationNew YorkNYUSA
| | - Clare M Miller
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Venugopalan D Nair
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Yongchao Ge
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Mary Anne S Amper
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Antonio Cappuccio
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | | | | | - Kristy Guevara
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Nada Marjanovic
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - German Nudelman
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Hanna Pincas
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Irene Ramos
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Rachel S G Sealfon
- Center for Computational Biology, Flatiron InstituteSimons FoundationNYNew YorkUSA
| | - Alessandra Soares‐Schanoski
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Present address:
Ragon Institute of MGH, MIT, and HarvardCambridgeMAUSA
| | - Sindhu Vangeti
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Mital Vasoya
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Dawn L Weir
- Naval Medical Research CenterMDSilver SpringUSA
| | - Elena Zaslavsky
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Seunghee Kim‐Schulze
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Sacha Gnjatic
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNYNew YorkUSA
- Human Immune Monitoring Center (HIMC)Icahn School of Medicine at Mount SinaiNYNew YorkUSA
| | | | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron InstituteSimons FoundationNYNew YorkUSA
- Department of Computer SciencePrinceton UniversityNJPrincetonUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityNJPrincetonUSA
| | - Stuart C Sealfon
- Department of NeurologyIcahn School of Medicine at Mount SinaiNYNew YorkUSA
| | - Maria Chikina
- Department of Computational and Systems Biology, School of MedicineUniversity of PittsburghPAPittsburghUSA
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6
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Alonso CAI, David CD, Toufaily C, Wang Y, Zhou X, Ongaro L, Nudelman G, Nair VD, Ruf-Zamojski F, Boehm U, Sealfon SC, Bernard DJ. Activating Transcription Factor 3 Stimulates Follicle-Stimulating Hormone-β Expression In Vitro But Is Dispensable for Follicle-Stimulating Hormone Production in Murine Gonadotropes In Vivo. Endocrinology 2023; 164:bqad050. [PMID: 36951304 PMCID: PMC10282924 DOI: 10.1210/endocr/bqad050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/24/2023]
Abstract
Follicle-stimulating hormone (FSH), a dimeric glycoprotein produced by pituitary gonadotrope cells, regulates spermatogenesis in males and ovarian follicle growth in females. Hypothalamic gonadotropin-releasing hormone (GnRH) stimulates FSHβ subunit gene (Fshb) transcription, though the underlying mechanisms are poorly understood. To address this gap in knowledge, we examined changes in pituitary gene expression in GnRH-deficient mice (hpg) treated with a regimen of exogenous GnRH that increases pituitary Fshb but not luteinizing hormone β (Lhb) messenger RNA levels. Activating transcription factor 3 (Atf3) was among the most upregulated genes. Activating transcription factor 3 (ATF3) can heterodimerize with members of the activator protein 1 family to regulate gene transcription. Co-expression of ATF3 with JunB stimulated murine Fshb, but not Lhb, promoter-reporter activity in homologous LβT2b cells. ATF3 also synergized with a constitutively active activin type I receptor to increase endogenous Fshb expression in these cells. Nevertheless, FSH production was intact in gonadotrope-specific Atf3 knockout [conditional knockout (cKO)] mice. Ovarian follicle development, ovulation, and litter sizes were equivalent between cKOs and controls. Testis weights and sperm counts did not differ between genotypes. Following gonadectomy, increases in LH secretion were enhanced in cKO animals. Though FSH levels did not differ between genotypes, post-gonadectomy increases in pituitary Fshb and gonadotropin α subunit expression were more pronounced in cKO than control mice. These data indicate that ATF3 can selectively stimulate Fshb expression in vitro but is not required for FSH production in vivo.
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Affiliation(s)
- Carlos A I Alonso
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Caroline D David
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Chirine Toufaily
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Ying Wang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Xiang Zhou
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Luisina Ongaro
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - German Nudelman
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ulrich Boehm
- Department of Experimental Pharmacology, Center for Molecular Signaling, Saarland University School of Medicine, Homburg 66421, Germany
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assay, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
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7
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Zhang Z, Sauerwald N, Cappuccio A, Ramos I, Nair VD, Nudelman G, Zaslavsky E, Ge Y, Gaitas A, Ren H, Brockman J, Geis J, Ramalingam N, King D, McClain MT, Woods CW, Henao R, Burke TW, Tsalik EL, Goforth CW, Lizewski RA, Lizewski SE, Weir DL, Letizia AG, Sealfon SC, Troyanskaya OG. Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease. Cell Rep Methods 2023; 3:100395. [PMID: 36936082 PMCID: PMC10014279 DOI: 10.1016/j.crmeth.2023.100395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/31/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection.
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Affiliation(s)
- Zijun Zhang
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Division of Artificial Intelligence in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, 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
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angelo Gaitas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hui Ren
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Joel Brockman
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Jennifer Geis
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | | | - David King
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | | | - Dawn L. Weir
- Naval Medical Research Center, Silver Spring, MD, USA
| | | | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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8
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Pai B, Tome‑Garcia J, Cheng WS, Nudelman G, Beaumont KG, Ghatan S, Panov F, Caballero E, Sarpong K, Marcuse L, Yoo J, Jiang Y, Schaefer A, Akbarian S, Sebra R, Pinto D, Zaslavsky E, Tsankova NM. Correction: High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy. Acta Neuropathol Commun 2022; 10:171. [DOI: 10.1186/s40478-022-01479-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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9
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Sauerwald N, Zhang Z, Ramos I, Nair VD, Soares-Schanoski A, Ge Y, Mao W, Alshammary H, Gonzalez-Reiche AS, van de Guchte A, Goforth CW, Lizewski RA, Lizewski SE, Amper MAS, Vasoya M, Seenarine N, Guevara K, Marjanovic N, Miller CM, Nudelman G, Schilling MA, Sealfon RSG, Termini MS, Vangeti S, Weir DL, Zaslavsky E, Chikina M, Wu YN, Van Bakel H, Letizia AG, Sealfon SC, Troyanskaya OG. Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection. Cell Syst 2022; 13:924-931.e4. [PMID: 36323307 PMCID: PMC9623453 DOI: 10.1016/j.cels.2022.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/21/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
Male sex is a major risk factor for SARS-CoV-2 infection severity. To understand the basis for this sex difference, we studied SARS-CoV-2 infection in a young adult cohort of United States Marine recruits. Among 2,641 male and 244 female unvaccinated and seronegative recruits studied longitudinally, SARS-CoV-2 infections occurred in 1,033 males and 137 females. We identified sex differences in symptoms, viral load, blood transcriptome, RNA splicing, and proteomic signatures. Females had higher pre-infection expression of antiviral interferon-stimulated gene (ISG) programs. Causal mediation analysis implicated ISG differences in number of symptoms, levels of ISGs, and differential splicing of CD45 lymphocyte phosphatase during infection. Our results indicate that the antiviral innate immunity set point causally contributes to sex differences in response to SARS-CoV-2 infection. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Zijun Zhang
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiguang Mao
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carl W Goforth
- Naval Medical Research Center, Silver Spring, MD 20910, USA
| | | | | | - Mary Anne S Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mital Vasoya
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nitish Seenarine
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristy Guevara
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nada Marjanovic
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Clare M Miller
- Department of Neurology, 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
| | | | - Rachel S G Sealfon
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Michael S Termini
- Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC 29902, USA
| | - Sindhu Vangeti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dawn L Weir
- Naval Medical Research Center, Silver Spring, MD 20910, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ying Nian Wu
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Harm Van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Department of Computer Science, Princeton University, Princeton, NJ 08540, USA.
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10
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Pai B, Tome-Garcia J, Cheng WS, Nudelman G, Beaumont KG, Ghatan S, Panov F, Caballero E, Sarpong K, Marcuse L, Yoo J, Jiang Y, Schaefer A, Akbarian S, Sebra R, Pinto D, Zaslavsky E, Tsankova NM. High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy. Acta Neuropathol Commun 2022; 10:149. [PMID: 36274170 PMCID: PMC9590125 DOI: 10.1186/s40478-022-01453-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The pathophysiology of epilepsy underlies a complex network dysfunction between neurons and glia, the molecular cell type-specific contributions of which remain poorly defined in the human disease. In this study, we validated a method that simultaneously isolates neuronal (NEUN +), astrocyte (PAX6 + NEUN–), and oligodendroglial progenitor (OPC) (OLIG2 + NEUN–) enriched nuclei populations from non-diseased, fresh-frozen human neocortex and then applied it to characterize the distinct transcriptomes of such populations isolated from electrode-mapped temporal lobe epilepsy (TLE) surgical samples. Nuclear RNA-seq confirmed cell type specificity and informed both common and distinct pathways associated with TLE in astrocytes, OPCs, and neurons. Compared to postmortem control, the transcriptome of epilepsy astrocytes showed downregulation of mature astrocyte functions and upregulation of development-related genes. To gain further insight into glial heterogeneity in TLE, we performed single cell transcriptomics (scRNA-seq) on four additional human TLE samples. Analysis of the integrated TLE dataset uncovered a prominent subpopulation of glia that express a hybrid signature of both reactive astrocyte and OPC markers, including many cells with a mixed GFAP + OLIG2 + phenotype. A further integrated analysis of this TLE scRNA-seq dataset and a previously published normal human temporal lobe scRNA-seq dataset confirmed the unique presence of hybrid glia only in TLE. Pseudotime analysis revealed cell transition trajectories stemming from this hybrid population towards both OPCs and reactive astrocytes. Immunofluorescence studies in human TLE samples confirmed the rare presence of GFAP + OLIG2 + glia, including some cells with proliferative activity, and functional analysis of cells isolated directly from these samples disclosed abnormal neurosphere formation in vitro. Overall, cell type-specific isolation of glia from surgical epilepsy samples combined with transcriptomic analyses uncovered abnormal glial subpopulations with de-differentiated phenotype, motivating further studies into the dysfunctional role of reactive glia in temporal lobe epilepsy.
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11
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Rubenstein AB, Hinkley JM, Nair VD, Nudelman G, Standley RA, Yi F, Yu G, Trappe TA, Bamman MM, Trappe SW, Sparks LM, Goodpaster BH, Vega RB, Sealfon SC, Zaslavsky E, Coen PM. Skeletal muscle transcriptome response to a bout of endurance exercise in physically active and sedentary older adults. Am J Physiol Endocrinol Metab 2022; 322:E260-E277. [PMID: 35068187 PMCID: PMC8897039 DOI: 10.1152/ajpendo.00378.2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Age-related declines in cardiorespiratory fitness and physical function are mitigated by regular endurance exercise in older adults. This may be due, in part, to changes in the transcriptional program of skeletal muscle following repeated bouts of exercise. However, the impact of chronic exercise training on the transcriptional response to an acute bout of endurance exercise has not been clearly determined. Here, we characterized baseline differences in muscle transcriptome and exercise-induced response in older adults who were active/endurance trained or sedentary. RNA-sequencing was performed on vastus lateralis biopsy specimens obtained before, immediately after, and 3 h following a bout of endurance exercise (40 min of cycling at 60%-70% of heart rate reserve). Using a recently developed bioinformatics approach, we found that transcript signatures related to type I myofibers, mitochondria, and endothelial cells were higher in active/endurance-trained adults and were associated with key phenotypic features including V̇o2peak, ATPmax, and muscle fiber proportion. Immune cell signatures were elevated in the sedentary group and linked to visceral and intermuscular adipose tissue mass. Following acute exercise, we observed distinct temporal transcriptional signatures that were largely similar among groups. Enrichment analysis revealed catabolic processes were uniquely enriched in the sedentary group at the 3-h postexercise timepoint. In summary, this study revealed key transcriptional signatures that distinguished active and sedentary adults, which were associated with difference in oxidative capacity and depot-specific adiposity. The acute response signatures were consistent with beneficial effects of endurance exercise to improve muscle health in older adults irrespective of exercise history and adiposity.NEW & NOTEWORTHY Muscle transcript signatures associated with oxidative capacity and immune cells underlie important phenotypic and clinical characteristics of older adults who are endurance trained or sedentary. Despite divergent phenotypes, the temporal transcriptional signatures in response to an acute bout of endurance exercise were largely similar among groups. These data provide new insight into the transcriptional programs of aging muscle and the beneficial effects of endurance exercise to promote healthy aging in older adults.
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Affiliation(s)
- Aliza B Rubenstein
- Department of Neurology, Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York
| | - German Nudelman
- Department of Neurology, Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Fanchao Yi
- AdventHealth Translational Research Institute, Orlando, Florida
| | - GongXin Yu
- AdventHealth Translational Research Institute, Orlando, Florida
| | - Todd A Trappe
- Human Performance Laboratory, Ball State University, Indianapolis, Indiana
| | - Marcas M Bamman
- Department of Cell, Developmental, and Integrative Biology, UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Scott W Trappe
- Human Performance Laboratory, Ball State University, Indianapolis, Indiana
| | - Lauren M Sparks
- AdventHealth Translational Research Institute, Orlando, Florida
| | | | - Rick B Vega
- AdventHealth Translational Research Institute, Orlando, Florida
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paul M Coen
- AdventHealth Translational Research Institute, Orlando, Florida
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12
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Joshi T, Nudelman G, Zaslavsky E, Tsankova N. EPCO-05. GENOME-WIDE ANALYSIS OF TEAD1 OCCUPANCY IN BIOLOGICALLY DISTINCT GLIOBLASTOMA SAMPLES. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.004] [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: 11/12/2022] Open
Abstract
Abstract
The diffusely infiltrative nature of glioblastoma (GBM) cells is a major contributor to the disease’s aggressive behavior, including its rapid progression and therapeutic resistance. Moreover, current treatment options do not target the invasive nature of GBM. Recent chromatin accessibility studies prioritized enrichment of the TEAD1 transcription factor motif in glioblastoma stem cell biology and subsequent knockout and overexpression studies confirmed a critical role for TEAD1 in GBM migration, in vitro and in vivo. However, the downstream mechanisms through which TEAD1 regulates GBM cell migration remain poorly understood. In this study, we performed chromatin immunoprecipitation (ChIP-seq) using TEAD1-specific antibody and IgG as non-specific binding control, to characterize TEAD1 occupancy across GBM samples with unique genomic alterations. ChIP-seq peaks were called using MACS2, filtered for duplicates and blacklisted regions, and normalized per sample to their respective genomic input. Initial functional enrichment analyses were performed on three GBM samples with the highest number of TEAD1 occupancy peaks using CistromeGO, which ranked genes based on their TEAD1-specific regulatory potential (RP) score, as a function of peak number and distance from the transcription start site. Analyses of the top 1000 genes with highest TEAD1 RP scores identified 132 common targets across all samples, including known TEAD target genes ETV1 and Cyr61, which related to angiogenesis, cadherin and integrin signaling, cell adhesion, and chromatin regulation gene ontology terms, among others. Interestingly, KEGG pathway analysis also revealed Hippo pathway enrichment across all GBM samples, suggesting a possible TEAD1 regulatory feedback loop in GBM. Analysis of TEAD1 ChIP-seq peaks in non-GBM negative control tissue did not show functional enrichment for any of the terms seen in the GBM samples. Ongoing analyses are focused on characterizing TEAD1 occupancy at active cis-regulatory regions using parallel H3K27ac ChIP-seq data, in order to prioritize the most salient TEAD1-regulatory targets in GBM.
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Affiliation(s)
- Tanvi Joshi
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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13
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Barrette AM, Ronk H, Joshi T, Mussa Z, Mehrotra M, Bouras A, Nudelman G, Jesu Raj JG, Bozec D, Lam W, Houldsworth J, Yong R, Zaslavsky E, Hadjipanayis CG, Birtwistle MR, Tsankova NM. Anti-invasive efficacy and survival benefit of the YAP-TEAD inhibitor Verteporfin in preclinical glioblastoma models. Neuro Oncol 2021; 24:694-707. [PMID: 34657158 DOI: 10.1093/neuonc/noab244] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) remains a largely incurable disease as current therapy fails to target the invasive nature of GBM growth in disease progression and recurrence. Here we use the FDA-approved drug and small molecule Hippo inhibitor Verteporfin to target YAP-TEAD activity, known to mediate convergent aspects of tumor invasion/metastasis, and assess the drug's efficacy and survival benefit in GBM models. METHODS Up to eight low-passage patient-derived GBM cell lines with distinct genomic drivers, including three primary/recurrent pairs, were treated with Verteporfin or vehicle to assess in-vitro effects on proliferation, migration, YAP-TEAD activity, and transcriptomics. Patient-derived orthotopic xenograft models (PDX) were used to assess Verteporfin's brain penetrance and effects on tumor burden and survival. RESULTS Verteporfin treatment disturbed YAP/TAZ-TEAD activity; disrupted transcriptome signatures related to invasion, epithelial-to-mesenchymal, and proneural-to-mesenchymal transition, phenocopying TEAD1-knockout effects; and impaired tumor migration/invasion dynamics across primary and recurrent GBM lines. In an aggressive orthotopic PDX GBM model, short-term Verteporfin treatment consistently diminished core and infiltrative tumor burden, which was associated with decreased tumor expression of Ki67, nuclear YAP, TEAD1, and TEAD-associated targets EGFR, CDH2 and ITGB1. Finally, long-term Verteporfin treatment appeared non-toxic and conferred survival benefit compared to vehicle in two PDX models: as monotherapy in primary (de-novo) GBM and in combination with Temozolomide chemoradiation in recurrent GBM, where VP treatment associated with increased MGMT methylation. CONCLUSIONS We demonstrate combined anti-invasive and anti-proliferative efficacy for Verteporfin with survival benefit in preclinical GBM models, indicating potential therapeutic value of this already FDA-approved drug if repurposed for glioblastoma patients.
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Affiliation(s)
- Anne Marie Barrette
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Halle Ronk
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tanvi Joshi
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zarmeen Mussa
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meenakshi Mehrotra
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandros Bouras
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joe G Jesu Raj
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dominique Bozec
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - William Lam
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jane Houldsworth
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raymund Yong
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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14
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Nudelman I, Kudrin D, Nudelman G, Deshpande R, Hartmann BM, Kleinstein SH, Myers CL, Sealfon SC, Zaslavsky E. Comparing Host Module Activation Patterns and Temporal Dynamics in Infection by Influenza H1N1 Viruses. Front Immunol 2021; 12:691758. [PMID: 34335598 PMCID: PMC8317020 DOI: 10.3389/fimmu.2021.691758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Influenza is a serious global health threat that shows varying pathogenicity among different virus strains. Understanding similarities and differences among activated functional pathways in the host responses can help elucidate therapeutic targets responsible for pathogenesis. To compare the types and timing of functional modules activated in host cells by four influenza viruses of varying pathogenicity, we developed a new DYNAmic MOdule (DYNAMO) method that addresses the need to compare functional module utilization over time. This integrative approach overlays whole genome time series expression data onto an immune-specific functional network, and extracts conserved modules exhibiting either different temporal patterns or overall transcriptional activity. We identified a common core response to influenza virus infection that is temporally shifted for different viruses. We also identified differentially regulated functional modules that reveal unique elements of responses to different virus strains. Our work highlights the usefulness of combining time series gene expression data with a functional interaction map to capture temporal dynamics of the same cellular pathways under different conditions. Our results help elucidate conservation of the immune response both globally and at a granular level, and provide mechanistic insight into the differences in the host response to infection by influenza strains of varying pathogenicity.
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Affiliation(s)
- Irina Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Division of General Internal Medicine, New York University Langone Medical Centre, New York, NY, United States
| | - Daniil Kudrin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Boris M Hartmann
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN, United States.,Program in Biomedical Informatics and Computational Biology, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Center for Advanced Research on Diagnostic Assays (CARDA), Icahn School of Medicine at Mount Sinai, New York, NY, United States
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15
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Ruf-Zamojski F, Zhang Z, Zamojski M, Smith GR, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon RG, Nair VD, Seenarine N, Amper MAS, Zhou X, Ongaro L, Toufaily C, Schang G, Nery JR, Bartlett A, Aldridge A, Jain N, Childs GV, Troyanskaya OG, Ecker JR, Turgeon JL, Welt CK, Bernard DJ, Sealfon SC. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun 2021; 12:2677. [PMID: 33976139 PMCID: PMC8113460 DOI: 10.1038/s41467-021-22859-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 06/06/2020] [Accepted: 03/16/2021] [Indexed: 11/12/2022] Open
Abstract
To provide a multi-omics resource and investigate transcriptional regulatory mechanisms, we profile the transcriptome, chromatin accessibility, and methylation status of over 70,000 single nuclei (sn) from adult mouse pituitaries. Paired snRNAseq and snATACseq datasets from individual animals highlight a continuum between developmental epigenetically-encoded cell types and transcriptionally-determined transient cell states. Co-accessibility analysis-based identification of a putative Fshb cis-regulatory domain that overlaps the fertility-linked rs11031006 human polymorphism, followed by experimental validation illustrate the use of this resource for hypothesis generation. We also identify transcriptional and chromatin accessibility programs distinguishing each major cell type. Regulons, which are co-regulated gene sets sharing binding sites for a common transcription factor driver, recapitulate cell type clustering. We identify both cell type-specific and sex-specific regulons that are highly correlated with promoter accessibility, but not with methylation state, supporting the centrality of chromatin accessibility in shaping cell-defining transcriptional programs. The sn multi-omics atlas is accessible at snpituitaryatlas.princeton.edu.
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Affiliation(s)
- Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA.
| | - Zidong Zhang
- Lewis-Sigler Institute for Integrative Genomics, and Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
| | - Michel Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Natalia Mendelev
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - German Nudelman
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Mika Moriwaki
- Division of Endocrinology and Metabolism, University of Utah, Salt Lake City, UT, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Rosa Gomez Castanon
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Nitish Seenarine
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Mary Anne S Amper
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Xiang Zhou
- Dept. of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Luisina Ongaro
- Dept. of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Chirine Toufaily
- Dept. of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Gauthier Schang
- Dept. of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Andrew Aldridge
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nimisha Jain
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA
| | - Gwen V Childs
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, and Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Judith L Turgeon
- Department of Internal Medicine, University of California, Davis, CA, USA
| | - Corrine K Welt
- Division of Endocrinology and Metabolism, University of Utah, Salt Lake City, UT, USA
| | - Daniel J Bernard
- Dept. of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY, USA.
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16
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Patel AS, Yoo S, Kong R, Sato T, Sinha A, Karam S, Bao L, Fridrikh M, Emoto K, Nudelman G, Powell CA, Beasley MB, Zhu J, Watanabe H. Prototypical oncogene family Myc defines unappreciated distinct lineage states of small cell lung cancer. Sci Adv 2021; 7:7/5/eabc2578. [PMID: 33514539 PMCID: PMC7846160 DOI: 10.1126/sciadv.abc2578] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 12/10/2020] [Indexed: 05/11/2023]
Abstract
Comprehensive genomic analyses of small cell lung cancer (SCLC) have revealed frequent mutually exclusive genomic amplification of MYC family members. Hence, it has been long suggested that they are functionally equivalent; however, more recently, their expression has been associated with specific neuroendocrine markers and distinct histopathology. Here, we explored a previously undescribed role of L-Myc and c-Myc as lineage-determining factors contributing to SCLC molecular subtypes and histology. Integrated transcriptomic and epigenomic analyses showed that L-Myc and c-Myc impart neuronal and non-neuroendocrine-associated transcriptional programs, respectively, both associated with distinct SCLC lineage. Genetic replacement of c-Myc with L-Myc in c-Myc-SCLC induced a neuronal state but was insufficient to induce ASCL1-SCLC. In contrast, c-Myc induced transition from ASCL1-SCLC to NEUROD1-SCLC characterized by distinct large-cell neuroendocrine carcinoma-like histopathology. Collectively, we characterize a role of historically defined general oncogenes, c-Myc and L-Myc, for regulating lineage plasticity across molecular and histological subtypes.
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Affiliation(s)
- Ayushi S Patel
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Ranran Kong
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Thoracic Surgery, The Second Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Takashi Sato
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Abhilasha Sinha
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah Karam
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Bao
- Ningxia People's Hospital, Yinchuan, Ningxia Province 750001, China
| | - Maya Fridrikh
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katsura Emoto
- Department of Diagnostic Pathology, Keio University Hospital, Tokyo 160-8582, Japan
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mary Beth Beasley
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jun Zhu
- Tisch Cancer Institute, 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
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Hideo Watanabe
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Tisch Cancer Institute, 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
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17
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Letizia AG, Ramos I, Obla A, Goforth C, Weir DL, Ge Y, Bamman MM, Dutta J, Ellis E, Estrella L, George MC, Gonzalez-Reiche AS, Graham WD, van de Guchte A, Gutierrez R, Jones F, Kalomoiri A, Lizewski R, Lizewski S, Marayag J, Marjanovic N, Millar EV, Nair VD, Nudelman G, Nunez E, Pike BL, Porter C, Regeimbal J, Rirak S, Santa Ana E, Sealfon RSG, Sebra R, Simons MP, Soares-Schanoski A, Sugiharto V, Termini M, Vangeti S, Williams C, Troyanskaya OG, van Bakel H, Sealfon SC. SARS-CoV-2 Transmission among Marine Recruits during Quarantine. N Engl J Med 2020; 383:2407-2416. [PMID: 33176093 PMCID: PMC7675690 DOI: 10.1056/nejmoa2029717] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND The efficacy of public health measures to control the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been well studied in young adults. METHODS We investigated SARS-CoV-2 infections among U.S. Marine Corps recruits who underwent a 2-week quarantine at home followed by a second supervised 2-week quarantine at a closed college campus that involved mask wearing, social distancing, and daily temperature and symptom monitoring. Study volunteers were tested for SARS-CoV-2 by means of quantitative polymerase-chain-reaction (qPCR) assay of nares swab specimens obtained between the time of arrival and the second day of supervised quarantine and on days 7 and 14. Recruits who did not volunteer for the study underwent qPCR testing only on day 14, at the end of the quarantine period. We performed phylogenetic analysis of viral genomes obtained from infected study volunteers to identify clusters and to assess the epidemiologic features of infections. RESULTS A total of 1848 recruits volunteered to participate in the study; within 2 days after arrival on campus, 16 (0.9%) tested positive for SARS-CoV-2, 15 of whom were asymptomatic. An additional 35 participants (1.9%) tested positive on day 7 or on day 14. Five of the 51 participants (9.8%) who tested positive at any time had symptoms in the week before a positive qPCR test. Of the recruits who declined to participate in the study, 26 (1.7%) of the 1554 recruits with available qPCR results tested positive on day 14. No SARS-CoV-2 infections were identified through clinical qPCR testing performed as a result of daily symptom monitoring. Analysis of 36 SARS-CoV-2 genomes obtained from 32 participants revealed six transmission clusters among 18 participants. Epidemiologic analysis supported multiple local transmission events, including transmission between roommates and among recruits within the same platoon. CONCLUSIONS Among Marine Corps recruits, approximately 2% who had previously had negative results for SARS-CoV-2 at the beginning of supervised quarantine, and less than 2% of recruits with unknown previous status, tested positive by day 14. Most recruits who tested positive were asymptomatic, and no infections were detected through daily symptom monitoring. Transmission clusters occurred within platoons. (Funded by the Defense Health Agency and others.).
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Affiliation(s)
- Andrew G Letizia
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Irene Ramos
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Ajay Obla
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Carl Goforth
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Dawn L Weir
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Yongchao Ge
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Marcas M Bamman
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Jayeeta Dutta
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Ethan Ellis
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Luis Estrella
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Mary-Catherine George
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Ana S Gonzalez-Reiche
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - William D Graham
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Adriana van de Guchte
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Ramiro Gutierrez
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Franca Jones
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Aspasia Kalomoiri
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Rhonda Lizewski
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Stephen Lizewski
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Jan Marayag
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Nada Marjanovic
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Eugene V Millar
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Venugopalan D Nair
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - German Nudelman
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Edgar Nunez
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Brian L Pike
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Chad Porter
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - James Regeimbal
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Stas Rirak
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Ernesto Santa Ana
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Rachel S G Sealfon
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Robert Sebra
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Mark P Simons
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Alessandra Soares-Schanoski
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Victor Sugiharto
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Michael Termini
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Sindhu Vangeti
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Carlos Williams
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Olga G Troyanskaya
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Harm van Bakel
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
| | - Stuart C Sealfon
- From the Naval Medical Research Center, Silver Spring (A.G.L., C.G., D.L.W., L.E., W.D.G., R.G., F.J., J.M., E.N., B.L.P., C.P., J.R., E.S.A., M.P.S., V.S., C.W.) and the Infectious Disease Clinical Research Program, Uniformed Services University (E.V.M.), Bethesda - both in Maryland; the Naval Medical Research Unit 6, Lima, Peru (R.L., S.L.); the Departments of Neurology (I.R., Y.G., M.-C.G., A.K., N.M., V.D.N., G.N., S.R., A.S.-S., S.V., S.C.S.) and Genetics and Genomic Sciences (A.O., J.D., E.E., A.S.G.-R., A.G., R.S., H.B.), Icahn Institute for Data Science and Genomic Technology (E.E., R.S., H.B.), the Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai (R.S.), and the Center for Computational Biology, Flatiron Institute (R.S.G.S., O.G.T.) - all in New York; the University of Alabama at Birmingham Center for Exercise Medicine, University of Alabama Medical School, Birmingham (M.M.B.); Sema4, Stamford, CT (R.S.); the Navy Medicine Readiness and Training Command Beaufort, Beaufort, SC (M.T.); and the Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ (O.G.T.)
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Cravedi P, Fribourg M, Zhang W, Yi Z, Zaslavsky E, Nudelman G, Anderson L, Hartzell S, Brouard S, Heeger PS. Distinct peripheral blood molecular signature emerges with successful tacrolimus withdrawal in kidney transplant recipients. Am J Transplant 2020; 20:3477-3485. [PMID: 32459070 PMCID: PMC7704683 DOI: 10.1111/ajt.15979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/17/2020] [Accepted: 04/25/2020] [Indexed: 01/25/2023]
Abstract
Tacrolimus (Tac) is an effective anti-rejection agent in kidney transplantation, but its off-target effects make withdrawal desirable. Although studies indicate that Tac can be safely withdrawn in a subset of kidney transplant recipients, immune mechanisms that underlie successful vs unsuccessful Tac removal are unknown. We performed microarray analyses of peripheral blood mononuclear cells (PBMC) RNA from subjects enrolled in the Clinical Trials in Organ Transplantation-09 study in which we randomized stable kidney transplant recipients to Tac withdrawal or maintenance of standard immunosuppression beginning 6 months after transplant. Eight of 14 subjects attempted but failed withdrawal, while six developed stable graft function for ≥2 years on mycophenolate mofetil plus prednisone. Whereas failed withdrawal upregulated immune activation genes, successful Tac withdrawal was associated with a downregulatory and proapoptotic gene program enriched within T cells. Functional analyses suggested stronger donor-reactive immunity in subjects who failed withdrawal without evidence of regulatory T cell dysfunction. Together, our data from a small, but unique, patient cohort support the conclusion that successful Tac withdrawal is not simply due to absence of donor-reactive immunity but rather is associated with an active immunological process.
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Affiliation(s)
- P. Cravedi
- Translational Transplant Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - M. Fribourg
- Translational Transplant Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - W Zhang
- Translational Transplant Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Z Yi
- Translational Transplant Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - E. Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - G. Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - L. Anderson
- Translational Transplant Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - S. Hartzell
- Translational Transplant Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sophie Brouard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation etImmunologie, Nantes, France
| | - P. S. Heeger
- Translational Transplant Research Center, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
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19
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Barrette AM, Bouras A, Nudelman G, Mussa Z, Zaslavsky E, Hadjipanayis C, Birtwistle M, Tsankova N. EXTH-51. ANTI-INVASIVE EFFICACY AND SURVIVAL BENEFIT OF THE YAP-TEAD INHIBITOR VERTEPORFIN IN PRECLINICAL GLIOBLASTOMA MODELS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.405] [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: 11/14/2022] Open
Abstract
Abstract
Glioblastoma (GBM) remains an incurable disease, in large part due to its malignant infiltrative spread, and current clinical therapy fails to target the invasive nature of tumor cells in disease progression and recurrence. Here, we use the YAP-TEAD inhibitor Verteporfin to target a convergence point for regulating tumor invasion/metastasis and establish the robust anti-invasive therapeutic efficacy of this FDA-approved drug and its survival benefit across several preclinical glioma models. Using patient-derived GBM cells and orthotopic xenograft models (PDX), we show that Verteporfin treatment disrupts YAP/TAZ-TEAD activity and processes related to cell adhesion, migration and epithelial-mesenchymal transition. In-vitro, Verteporfin impairs tumor migration, invasion and motility dynamics. In-vivo, intraperitoneal administration of Verteporfin in mice with orthotopic PDX tumors shows consistent drug accumulation within the brain and decreased infiltrative tumor burden, across three independent experiments. Interestingly, PDX tumors with impaired invasion after Verteporfin treatment downregulate CDH2 and ITGB1 adhesion protein levels within the tumor microenvironment. Finally, Verteporfin treatment confers survival benefit in two independent PDX models: as monotherapy in de-novo GBM and in combination with standard-of-care chemoradiation in recurrent GBM. These findings indicate potential therapeutic value of this FDA-approved drug if repurposed for GBM patients.
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Affiliation(s)
| | | | | | - Zarmeen Mussa
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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20
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Barrette AM, Bouras A, Nudelman G, Bozec D, Shakawat N, Zaslavsky E, Hadjipanayis C, Birtwistle MR, Tsankova NM. Abstract 1111: Verteporfin inhibits GBM growth and migration and confers survival benefit in xenograft models. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1111] [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
The diffusely infiltrative growth and spread, complex molecular and oncogenic signaling aberrations, and inter-and intra-tumoral heterogeneity in glioblastoma (GBM) impedes gross-total resection and chemoradiation and highlight the need for improved tumor-specific brain-penetrant therapies that inhibit cell migration in addition to proliferation. Invasive GBM cells undergo an epithelial-mesenchymal transition (EMT) phenotypic switch, expressing higher levels of genes involved in EMT remodeling, survival, and immune response compared to non-invasive GBM tumor cells. Recently, our lab defined a regulatory chromatin accessibility signature centered around the TEAD transcriptional family, which relates specifically to tumor migration in uncultured, patient-derived GBM stem cell populations, and we functionally validated TEAD1 as a driver of GBM migration and EMT, both in vitro and in vivo. The TEAD family of transcription factors, along with their co-activators YAP/TAZ, are the main downstream effectors of the Hippo pathway, a regulator of tissue growth and cell fate whose dysregulation has been implicated in tumor invasion, metastasis, and chemoresistance in other solid tumors. Here we explored the therapeutic efficacy of Verteporfin (VP), an FDA-approved macular degeneration therapy, and a small-molecule inhibitor of the YAP/TEAD complex, in patient-derived GBM cells and orthotopic xenotransplant mouse models (PDX), assessing VP's impact on GBM proliferation and migration both in vitro and in vivo. VP treatment across three different cell lines inhibited not only glioma growth but also significantly impaired tumor migration in three different in vitro assays (live cell tracking, transwell invasion, and spheroid dispersion) in a dose-dependent manner. At the protein and whole transcriptomic levels, VP-treated cells showed dose-dependent downregulation of TEAD-target activity and significant downregulation of EMT and cell migration functional gene sets, compared to vehicle. In several independent in vivo experiments, intraperitoneal administration of VP in mice with aggressive PDX glioblastoma showed consistent drug penetration into the brain parenchyma without systemic toxicity, resulted in lower tumor burden both at the tumor core and the leading infiltrative edge (n=22 VP, n=21 VEH, p=0.02, each), showed decreased number of individual distal migratory tumor cells (n=6 VP, n=5 VEH, p=0.0001 / n=6 VP, n=5 VEH, p=0.04), and, notably, conferred a survival benefit in combination with TMZ and radiation (n=10 per condition, p=0.02). Furthermore, in PDX mice transplanted with a more typical GBM, daily administration of VP for up to 280 days conferred survival benefit even as monotherapy (n=8 per condition, p=0.02), in the absence of systemic toxicity. The inhibitory effect of Verteporfin on downstream YAP/TEAD signaling and GBM migration, and its brain penetrance at non-toxic levels, underscore potential future therapeutic value and repurposing of this drug in GBM patients.
Citation Format: Anne Marie Barrette, Alexandros Bouras, German Nudelman, Dominique Bozec, Noshin Shakawat, Elena Zaslavsky, Constantinos Hadjipanayis, Marc R. Birtwistle, Nadejda M. Tsankova. Verteporfin inhibits GBM growth and migration and confers survival benefit in xenograft models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1111.
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Patel AS, Yoo S, Kong R, Sato T, Fridrikh M, Nudelman G, Powell CA, Zhu J, Watanabe H. Abstract 1295: Myc family members differentially regulate lineage plasticity in small cell lung cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1295] [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
Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer with a dismal prognosis. The standard-of-care remains to be uniform treatment with chemotherapy and radiotherapy, while emerging evidence suggests its molecular heterogeneity that has been previously under-appreciated. In primary SCLC, the gene loci for Myc family members are amplified mutually exclusively, their expression is correlated with unique neuroendocrine markers and distinct histopathology of xenografts from SCLC cell lines and murine SCLC. In this study, we use integrative genomic and epigenomic analyses to explore a novel role for c-Myc and L-Myc as lineage determining factors to bridge the gap between SCLC molecular subtypes and histological classification. First, we built a novel network using the Bayesian estimation from combined mRNA expression profile datasets for a total of 135 primary SCLC tumors. This revealed distinct transcriptional networks for c-Myc and L-Myc; wherein L-Myc was enriched for neuronal pathways and c-Myc for Notch signaling and epithelial-to-mesenchymal transition. The assay for transposase accessible-chromatin profiling of 3 representative cell lines for each c-Myc and L-Myc, revealed enrichment of biological processes involved in neuronal development for L-Myc expressing cell lines and active Notch signaling in c-Myc expressing cell lines. Together, these analyses implied that c-Myc and L-Myc govern distinct transcriptional programs to impart respective transcriptional networks associated with features unique to SCLC molecular subtypes. Next, we genetically engineered c-Myc amplified SCLC to exchange c-Myc with L-Myc and found L-Myc regulates neuronal associated pathways but was insufficient to induce lineage switch, however; c-Myc was required for the maintenance of NeuroD1-driven lineage state. In contrast, exogenous expression of c-Myc in classical-ASCL1-positive SCLC revealed incompatibility of c-Myc expression in this subtype, and led to suppression of neuronal associated pathways, trans-differentiation to NeuroD1-SCLC accompanied by variant histopathological features.
Pharmacological inhibition of neuroendocrine-low associated Notch signaling and its target RE-1 silencing transcription factor (REST), revealed c-Myc-induced suppression of ASCL1 is not mediated by Notch signaling but rather by direct activation of REST expression. Collectively, our findings reveal a previously undescribed role for historically defined general oncogenes, c-Myc and L-Myc, in regulating lineage plasticity across SCLC molecular subtypes as well as histological classes.
Citation Format: Ayushi S. Patel, Seungyeul Yoo, Ranran Kong, Takashi Sato, Maya Fridrikh, German Nudelman, Charles A. Powell, Jun Zhu, Hideo Watanabe. Myc family members differentially regulate lineage plasticity in small cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1295.
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Affiliation(s)
| | - Seungyeul Yoo
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ranran Kong
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Takashi Sato
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Maya Fridrikh
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - Jun Zhu
- Icahn School of Medicine at Mount Sinai, New York, NY
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22
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Sanford JA, Nogiec CD, Lindholm ME, Adkins JN, Amar D, Dasari S, Drugan JK, Fernández FM, Radom-Aizik S, Schenk S, Snyder MP, Tracy RP, Vanderboom P, Trappe S, Walsh MJ, Adkins JN, Amar D, Dasari S, Drugan JK, Evans CR, Fernandez FM, Li Y, Lindholm ME, Nogiec CD, Radom-Aizik S, Sanford JA, Schenk S, Snyder MP, Tomlinson L, Tracy RP, Trappe S, Vanderboom P, Walsh MJ, Lee Alekel D, Bekirov I, Boyce AT, Boyington J, Fleg JL, Joseph LJ, Laughlin MR, Maruvada P, Morris SA, McGowan JA, Nierras C, Pai V, Peterson C, Ramos E, Roary MC, Williams JP, Xia A, Cornell E, Rooney J, Miller ME, Ambrosius WT, Rushing S, Stowe CL, Jack Rejeski W, Nicklas BJ, Pahor M, Lu CJ, Trappe T, Chambers T, Raue U, Lester B, Bergman BC, Bessesen DH, Jankowski CM, Kohrt WM, Melanson EL, Moreau KL, Schauer IE, Schwartz RS, Kraus WE, Slentz CA, Huffman KM, Johnson JL, Willis LH, Kelly L, Houmard JA, Dubis G, Broskey N, Goodpaster BH, Sparks LM, Coen PM, Cooper DM, Haddad F, Rankinen T, Ravussin E, Johannsen N, Harris M, Jakicic JM, Newman AB, Forman DD, Kershaw E, Rogers RJ, Nindl BC, Page LC, Stefanovic-Racic M, Barr SL, Rasmussen BB, Moro T, Paddon-Jones D, Volpi E, Spratt H, Musi N, Espinoza S, Patel D, Serra M, Gelfond J, Burns A, Bamman MM, Buford TW, Cutter GR, Bodine SC, Esser K, Farrar RP, Goodyear LJ, Hirshman MF, Albertson BG, Qian WJ, Piehowski P, Gritsenko MA, Monore ME, Petyuk VA, McDermott JE, Hansen JN, Hutchison C, Moore S, Gaul DA, Clish CB, Avila-Pacheco J, Dennis C, Kellis M, Carr S, Jean-Beltran PM, Keshishian H, Mani D, Clauser K, Krug K, Mundorff C, Pearce C, Ivanova AA, Ortlund EA, Maner-Smith K, Uppal K, Zhang T, Sealfon SC, Zaslavsky E, Nair V, Li S, Jain N, Ge Y, Sun Y, Nudelman G, Ruf-zamojski F, Smith G, Pincas N, Rubenstein A, Anne Amper M, Seenarine N, Lappalainen T, Lanza IR, Sreekumaran Nair K, Klaus K, Montgomery SB, Smith KS, Gay NR, Zhao B, Hung CJ, Zebarjadi N, Balliu B, Fresard L, Burant CF, Li JZ, Kachman M, Soni T, Raskind AB, Gerszten R, Robbins J, Ilkayeva O, Muehlbauer MJ, Newgard CB, Ashley EA, Wheeler MT, Jimenez-Morales D, Raja A, Dalton KP, Zhen J, Suk Kim Y, Christle JW, Marwaha S, Chin ET, Hershman SG, Hastie T, Tibshirani R, Rivas MA. Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell 2020; 181:1464-1474. [DOI: 10.1016/j.cell.2020.06.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
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Ruf-Zamojski FM, Zamojski MA, Nudelman G, Ge Y, Mendelev N, Smith GR, Zhou X, Toufaily C, Schang G, Gambino LO, Liu H, Gomez Castanon RG, Moriwaki M, Nair V, Pincas H, Nery JR, Bartlett A, Alridge A, Odle AK, Childs GV, Turgeon JL, Welt CK, Ecker JR, Bernard DJ, Sealfon SC. SAT-298 Integrative Single-Cell Transcriptomic and Epigenomic Landscape of Mouse Anterior Pituitary Cell Types. J Endocr Soc 2020. [PMCID: PMC7209186 DOI: 10.1210/jendso/bvaa046.593] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Abstract
The pituitary gland is a critical regulator of the neuroendocrine system. To further our understanding of the classification, cellular heterogeneity, and regulatory landscape of pituitary cell types, we performed and computationally integrated single cell (SC)/single nucleus (SN) resolution experiments capturing RNA expression, chromatin accessibility, and DNA methylation state from mouse dissociated whole pituitaries. Both SC and SN transcriptome analysis and promoter accessibility identified the five classical hormone-producing cell types (somatotropes, gonadotropes (GT), lactotropes, thyrotropes, and corticotropes). GT cells distinctively expressed transcripts for Cga, Fshb, Lhb, Nr5a1, and Gnrhr in SC RNA-seq and SN RNA-seq. This was matched in SN ATAC-seq with GTs specifically showing open chromatin at the promoter regions for the same genes. Similarly, the other classically defined anterior pituitary cells displayed transcript expression and chromatin accessibility patterns characteristic of their own cell type. This integrated analysis identified additional cell-types, such as a stem cell cluster expressing transcripts for Sox2, Sox9, Mia, and Rbpms, and a broadly accessible chromatin state. In addition, we performed bulk ATAC-seq in the LβT2b gonadotrope-like cell line. While the FSHB promoter region was closed in the cell line, we identified a region upstream of Fshb that became accessible by the synergistic actions of GnRH and activin A, and that corresponded to a conserved region identified by a polycystic ovary syndrome (PCOS) single nucleotide polymorphism (SNP). Although this locus appears closed in deep sequencing bulk ATAC-seq of dissociated mouse pituitary cells, SN ATAC-seq of the same preparation showed that this site was specifically open in mouse GT, but closed in 14 other pituitary cell type clusters. This discrepancy highlighted the detection limit of a bulk ATAC-seq experiment in a subpopulation, as GT represented ~5% of this dissociated anterior pituitary sample. These results identified this locus as a candidate for explaining the dual dependence of Fshb expression on GnRH and activin/TGFβ signaling, and potential new evidence for upstream regulation of Fshb. The pituitary epigenetic landscape provides a resource for improved cell type identification and for the investigation of the regulatory mechanisms driving cell-to-cell heterogeneity.
Additional authors not listed due to abstract submission restrictions: N. Seenarine, M. Amper, N. Jain (ISMMS).
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Affiliation(s)
| | | | | | - Yongchao Ge
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | | | | | | | - Hanqing Liu
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | | | - Hanna Pincas
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph R Nery
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anna Bartlett
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Andrew Alridge
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Gwen V Childs
- Univ of AR Med Sci/Coll of Med, Little Rock, AR, USA
| | | | | | - Joseph R Ecker
- The Salk Institute for Biological Studies, La Jolla, CA, USA
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24
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Tome-Garcia J, Erfani P, Nudelman G, Tejero R, Friedel R, Zaslavsky E, Tsankova N. ANGI-04. TEAD1 REGULATES CELL MIGRATION IN HUMAN GLIOBLASTOMA IN PART THROUGH EMT-ASSOCIATED CADHERINS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.106] [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: 11/12/2022] Open
Affiliation(s)
- Jessica Tome-Garcia
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Parsa Erfani
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rut Tejero
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roland Friedel
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nadejda Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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25
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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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26
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Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI. DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle 2018; 17:348-355. [PMID: 29139326 DOI: 10.1080/15384101.2017.1404208] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.
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Affiliation(s)
- Igor B Rogozin
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Alexander Goncearenco
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Artem G Lada
- b Department Microbiology and Molecular Genetics , University of California , Davis , CA , USA
| | - Subhajyoti De
- c Rutgers Cancer Institute of New Jersey , Rutgers University , New Brunswick , NJ , USA
| | - Vyacheslav Yurchenko
- d Life Science Research Center , University of Ostrava, 71000 Ostrava , Czech Republic
| | - German Nudelman
- e Systems Biology Center , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , USA
| | - Anna R Panchenko
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - David N Cooper
- f Institute of Medical Genetics, School of Medicine , Cardiff University , UK
| | - Youri I Pavlov
- g Eppley Institute for Research in Cancer and Allied Diseases , University of Nebraska Medical Center , Omaha , NE 68198, USA.,h Departments of Microbiology and Pathology , University of Nebraska Medical Center , Omaha , NE , USA.,i Biochemistry and Molecular Biology , University of Nebraska Medical Center , Omaha , NE , USA.,j Genetics, Cell Biology and Anatomy , University of Nebraska Medical Center , Omaha , NE , USA
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Ruf-Zamojski F, Fribourg M, Ge Y, Nair V, Pincas H, Zaslavsky E, Nudelman G, Tuminello SJ, Watanabe H, Turgeon JL, Sealfon SC. Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone. Front Endocrinol (Lausanne) 2018; 9:34. [PMID: 29487567 PMCID: PMC5816955 DOI: 10.3389/fendo.2018.00034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/24/2018] [Indexed: 12/26/2022] Open
Abstract
The LβT2 mouse pituitary cell line has many characteristics of a mature gonadotrope and is a widely used model system for studying the developmental processes and the response to gonadotropin-releasing hormone (GnRH). The global epigenetic landscape, which contributes to cell-specific gene regulatory mechanisms, and the single-cell transcriptome response variation of LβT2 cells have not been previously investigated. Here, we integrate the transcriptome and genome-wide chromatin accessibility state of LβT2 cells during GnRH stimulation. In addition, we examine cell-to-cell variability in the transcriptional response to GnRH using Gel bead-in-Emulsion Drop-seq technology. Analysis of a bulk RNA-seq data set obtained 45 min after exposure to either GnRH or vehicle identified 112 transcripts that were regulated >4-fold by GnRH (FDR < 0.05). The top regulated transcripts constitute, as determined by Bayesian massive public data integration analysis, a human pituitary-relevant coordinated gene program. Chromatin accessibility [assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq)] data sets generated from GnRH-treated LβT2 cells identified more than 58,000 open chromatin regions, some containing notches consistent with bound transcription factor footprints. The study of the most prominent open regions showed that 75% were in transcriptionally active promoters or introns, supporting their involvement in active transcription. Lhb, Cga, and Egr1 showed significantly open chromatin over their promoters. While Fshb was closed over its promoter, several discrete significantly open regions were found at -40 to -90 kb, which may represent novel upstream enhancers. Chromatin accessibility determined by ATAC-seq was associated with high levels of gene expression determined by RNA-seq. We obtained high-quality single-cell Gel bead-in-Emulsion Drop-seq transcriptome data, with an average of >4,000 expressed genes/cell, from 1,992 vehicle- and 1,889 GnRH-treated cells. While the individual cell expression patterns showed high cell-to-cell variation, representing both biological and measurement variation, the average expression patterns correlated well with bulk RNA-seq data. Computational assignment of each cell to its precise cell cycle phase showed that the response to GnRH was unaffected by cell cycle. To our knowledge, this study represents the first genome-wide epigenetic and single-cell transcriptomic characterization of this important gonadotrope model. The data have been deposited publicly and should provide a resource for hypothesis generation and further study.
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Affiliation(s)
- Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Miguel Fribourg
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Venugopalan Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Elena Zaslavsky
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
| | - German Nudelman
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Stephanie J. Tuminello
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Hideo Watanabe
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | | | - Stuart C. Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, United States
- Departments of Neuroscience and Pharmacological Sciences, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- *Correspondence: Stuart C. Sealfon,
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28
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Hartmann BM, Albrecht RA, Zaslavsky E, Nudelman G, Pincas H, Marjanovic N, Schotsaert M, Martínez-Romero C, Fenutria R, Ingram JP, Ramos I, Fernandez-Sesma A, Balachandran S, García-Sastre A, Sealfon SC. Pandemic H1N1 influenza A viruses suppress immunogenic RIPK3-driven dendritic cell death. Nat Commun 2017; 8:1931. [PMID: 29203926 PMCID: PMC5715119 DOI: 10.1038/s41467-017-02035-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 06/17/2016] [Accepted: 11/02/2017] [Indexed: 12/15/2022] Open
Abstract
The risk of emerging pandemic influenza A viruses (IAVs) that approach the devastating 1918 strain motivates finding strain-specific host–pathogen mechanisms. During infection, dendritic cells (DC) mature into antigen-presenting cells that activate T cells, linking innate to adaptive immunity. DC infection with seasonal IAVs, but not with the 1918 and 2009 pandemic strains, induces global RNA degradation. Here, we show that DC infection with seasonal IAV causes immunogenic RIPK3-mediated cell death. Pandemic IAV suppresses this immunogenic DC cell death. Only DC infected with seasonal IAV, but not with pandemic IAV, enhance maturation of uninfected DC and T cell proliferation. In vivo, circulating T cell levels are reduced after pandemic, but not seasonal, IAV infection. Using recombinant viruses, we identify the HA genomic segment as the mediator of cell death inhibition. These results show how pandemic influenza viruses subvert the immune response. The differences in virus-host interactions resulting in distinct pathogenicity of seasonal and pandemic influenza A viruses (IAV) are not well understood. Here, the authors show that the hemagglutinin segment from pandemic, but not seasonal, IAV suppresses RIPK3-mediated dendritic cell death, thereby reducing T cell activation.
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Affiliation(s)
- Boris M Hartmann
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Randy A Albrecht
- Department of Microbiology and Global Health & Emerging Pathogens 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
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hanna Pincas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nada Marjanovic
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Schotsaert
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carles Martínez-Romero
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rafael Fenutria
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Irene Ramos
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Adolfo García-Sastre
- Department of Microbiology and Global Health & Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Tsankova N, Erfani P, Tome-Garcia J, Nudelman G, Tsankov A, Walsh M, Zaslavsky E. GENE-11. CHROMATIN ACCESSIBILITY DEFINES TRANSCRIPTIONAL DRIVERS OF MIGRATION IN HUMAN GLIOBLASTOMA. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Tome-Garcia J, Tejero R, Nudelman G, Yong RL, Sebra R, Wang H, Fowkes M, Magid M, Walsh M, Silva-Vargas V, Zaslavsky E, Friedel RH, Doetsch F, Tsankova NM. Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR + Populations with Stem Cell Properties. Stem Cell Reports 2017; 8:1421-1429. [PMID: 28434940 PMCID: PMC5425658 DOI: 10.1016/j.stemcr.2017.03.019] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 03/17/2017] [Accepted: 03/17/2017] [Indexed: 11/20/2022] Open
Abstract
Characterization of non-neoplastic and malignant human stem cell populations in their native state can provide new insights into gliomagenesis. Here we developed a purification strategy to directly isolate EGFR+/- populations from human germinal matrix (GM) and adult subventricular zone autopsy tissues, and from de novo glioblastoma (GBM) resections, enriching for cells capable of binding EGF ligand (LBEGFR+), and uniquely compared their functional and molecular properties. LBEGFR+ populations in both GM and GBM encompassed all sphere-forming cells and displayed proliferative stem cell properties in vitro. In xenografts, LBEGFR+ GBM cells showed robust tumor initiation and progression to high-grade, infiltrative gliomas. Whole-transcriptome sequencing analysis confirmed enrichment of proliferative pathways in both developing and neoplastic freshly isolated EGFR+ populations, and identified both unique and shared sets of genes. The ability to prospectively isolate stem cell populations using native ligand-binding capacity opens new doors onto understanding both normal human development and tumor cell biology.
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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, Friedman Brain Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rut Tejero
- Department of Neuroscience, Friedman Brain Institute, Tisch Cancer 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
| | - Raymund L Yong
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Pharmacological Sciences, Center for RNA Biology and Medicine and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Huaien Wang
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mary Fowkes
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Margret Magid
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin Walsh
- Department of Pharmacological Sciences, Center for RNA Biology and Medicine and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Violeta Silva-Vargas
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Roland H Friedel
- Department of Neuroscience, Friedman Brain Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fiona Doetsch
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Biozentrum, University of Basel, Basel 4056, Switzerland
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Friedman Brain Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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31
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Tome-Garcia J, Tejero-Villalba R, Zaslavsky E, Nudelman G, Yong R, Walsch M, Friedel R, Doetsch F, Tsankova N. STMC-28. INTACT EGFR DEFINES HUMAN GERMINAL MATRIX AND GLIOBLASTOMA POPULATIONS WITH SHARED AND EPIGENETICALLY IMPRINTED STEM CELL PROPERTIES. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now212.791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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32
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Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC. MOCCASIN: converting MATLAB ODE models to SBML. Bioinformatics 2016; 32:1905-6. [PMID: 26861819 PMCID: PMC4908318 DOI: 10.1093/bioinformatics/btw056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/25/2016] [Indexed: 11/29/2022] Open
Abstract
Summary: MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging—especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format. Availability and implementation: MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin. Contact: mhucka@caltech.edu Supplementary information: More information is available at https://github.com/sbmlteam/moccasin.
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Affiliation(s)
- Harold F Gómez
- Department of Biosystems Science and Engineering, ETH Zürich, Basel CH 4058, Switzerland
| | - Michael Hucka
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah M Keating
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, UK and
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, Mount Sinai Medical Center and School of Medicine, New York, NY 10029, USA
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel CH 4058, Switzerland
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, Mount Sinai Medical Center and School of Medicine, New York, NY 10029, USA
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33
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Fribourg Casajuana ML, Hartmann BM, Tabbaa OP, Ramos I, Zaslavsky E, Nudelman G, Albrecht RA, Merad M, Hayot F, Jayaprakash C, Kleinstein SH, Garcia-Sastre A, Sealfon SC. Single cell variability in pro-inflammatory and antiviral gene responses in dendritic cells. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.202.29] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Type I interferons (IFNs) can have both protective and deleterious effects in chronic infection and autoimmune disease. Cellular responses to type I IFNs are mediated by IFN-stimulated genes (ISGs), are cell type-dependent, and likely cell specific. Varying responses of individual cells to immune signals, such as type I IFNs, may be critical in orchestrating context and microenvironment appropriate immune responses. Simulations of an agent-based mathematical model of viral infection suggested that within each cell, the levels of pro-inflammatory ISGs induced by STAT dimers and the antiviral ISGs induced by the ISGF-3 heterotrimer can show low correlation. We used RNAseq to study global single-cell correlation of ISG groups in human peripheral blood CD1c+ dendritic cells infected with an influenza A H1N1 virus. Consonant with the simulations, distinct groups of ISGs were identified that showed high levels of single cell expression correlation within, but low to negative correlations across ISG subgroups. Using multiple probe FISH we find low single cell correlation of the pro-inflammatory ISG IL6 and the antiviral ISG RIG-I induction in cells stimulated with type I IFN. The single cell correlations in the induction of the two genes were 0.56, 0.55 and 0.19 in human peripheral blood plasmacytoid dendritic cells, monocytes, and monocyte-derived dendritic cells respectively. The generation of uncorrelated pro-inflammatory and antiviral ISG single cell responses within a dendritic cell population can increase the breadth of the immune response to noxious stimuli.
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Laitman BM, Asp L, Mariani JN, Zhang J, Liu J, Sawai S, Chapouly C, Horng S, Kramer EG, Mitiku N, Loo H, Burlant N, Pedre X, Hara Y, Nudelman G, Zaslavsky E, Lee YM, Braun DA, Lu QR, Narla G, Raine CS, Friedman SL, Casaccia P, John GR. The Transcriptional Activator Krüppel-like Factor-6 Is Required for CNS Myelination. PLoS Biol 2016; 14:e1002467. [PMID: 27213272 PMCID: PMC4877075 DOI: 10.1371/journal.pbio.1002467] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/22/2016] [Indexed: 12/31/2022] Open
Abstract
Growth factors of the gp130 family promote oligodendrocyte differentiation, and viability, and myelination, but their mechanisms of action are incompletely understood. Here, we show that these effects are coordinated, in part, by the transcriptional activator Krüppel-like factor-6 (Klf6). Klf6 is rapidly induced in oligodendrocyte progenitors (OLP) by gp130 factors, and promotes differentiation. Conversely, in mice with lineage-selective Klf6 inactivation, OLP undergo maturation arrest followed by apoptosis, and CNS myelination fails. Overlapping transcriptional and chromatin occupancy analyses place Klf6 at the nexus of a novel gp130-Klf-importin axis, which promotes differentiation and viability in part via control of nuclear trafficking. Klf6 acts as a gp130-sensitive transactivator of the nuclear import factor importin-α5 (Impα5), and interfering with this mechanism interrupts step-wise differentiation. Underscoring the significance of this axis in vivo, mice with conditional inactivation of gp130 signaling display defective Klf6 and Impα5 expression, OLP maturation arrest and apoptosis, and failure of CNS myelination.
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Affiliation(s)
- Benjamin M. Laitman
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Linnéa Asp
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - John N. Mariani
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jingya Zhang
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jia Liu
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Setsu Sawai
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Candice Chapouly
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sam Horng
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Elisabeth G. Kramer
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Nesanet Mitiku
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Hannah Loo
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Natalie Burlant
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Xiomara Pedre
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yuko Hara
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - German Nudelman
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Systems Biology Center, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Elena Zaslavsky
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Systems Biology Center, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Young-Min Lee
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - David A. Braun
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Systems Biology Center, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Q. Richard Lu
- Pediatrics, Cincinnati Childrens’ Hospital, Cincinnati, Ohio, United States of America
| | - Goutham Narla
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Cedric S. Raine
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Scott L. Friedman
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Patrizia Casaccia
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Gareth R. John
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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Chapouly C, Tadesse Argaw A, Horng S, Castro K, Zhang J, Asp L, Loo H, Laitman BM, Mariani JN, Straus Farber R, Zaslavsky E, Nudelman G, Raine CS, John GR. Astrocytic TYMP and VEGFA drive blood-brain barrier opening in inflammatory central nervous system lesions. Brain 2015; 138:1548-67. [PMID: 25805644 DOI: 10.1093/brain/awv077] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/26/2015] [Indexed: 12/21/2022] Open
Abstract
In inflammatory central nervous system conditions such as multiple sclerosis, breakdown of the blood-brain barrier is a key event in lesion pathogenesis, predisposing to oedema, excitotoxicity, and ingress of plasma proteins and inflammatory cells. Recently, we showed that reactive astrocytes drive blood-brain barrier opening, via production of vascular endothelial growth factor A (VEGFA). Here, we now identify thymidine phosphorylase (TYMP; previously known as endothelial cell growth factor 1, ECGF1) as a second key astrocyte-derived permeability factor, which interacts with VEGFA to induce blood-brain barrier disruption. The two are co-induced NFκB1-dependently in human astrocytes by the cytokine interleukin 1 beta (IL1B), and inactivation of Vegfa in vivo potentiates TYMP induction. In human central nervous system microvascular endothelial cells, VEGFA and the TYMP product 2-deoxy-d-ribose cooperatively repress tight junction proteins, driving permeability. Notably, this response represents part of a wider pattern of endothelial plasticity: 2-deoxy-d-ribose and VEGFA produce transcriptional programs encompassing angiogenic and permeability genes, and together regulate a third unique cohort. Functionally, each promotes proliferation and viability, and they cooperatively drive motility and angiogenesis. Importantly, introduction of either into mouse cortex promotes blood-brain barrier breakdown, and together they induce severe barrier disruption. In the multiple sclerosis model experimental autoimmune encephalitis, TYMP and VEGFA co-localize to reactive astrocytes, and correlate with blood-brain barrier permeability. Critically, blockade of either reduces neurologic deficit, blood-brain barrier disruption and pathology, and inhibiting both in combination enhances tissue preservation. Suggesting importance in human disease, TYMP and VEGFA both localize to reactive astrocytes in multiple sclerosis lesion samples. Collectively, these data identify TYMP as an astrocyte-derived permeability factor, and suggest TYMP and VEGFA together promote blood-brain barrier breakdown.
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Affiliation(s)
- Candice Chapouly
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Azeb Tadesse Argaw
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Sam Horng
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Kamilah Castro
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Jingya Zhang
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Linnea Asp
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Hannah Loo
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Benjamin M Laitman
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - John N Mariani
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Rebecca Straus Farber
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Elena Zaslavsky
- 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 4 Department of Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - German Nudelman
- 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 4 Department of Systems Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Cedric S Raine
- 5 Department of Pathology (Neuropathology), Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gareth R John
- 1 Corinne Goldsmith Dickinson Centre for MS, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 2 Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA 3 Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
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Hartmann BM, Marjanovic N, Nudelman G, Moran TM, Sealfon SC. Combinatorial cytokine code generates anti-viral state in dendritic cells. Front Immunol 2014; 5:73. [PMID: 24616721 PMCID: PMC3935347 DOI: 10.3389/fimmu.2014.00073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
The physiological function of the immune system and the response to therapeutic immunomodulators may be sensitive to combinatorial cytokine micro-environments that shape the responses of specific immune cells. Previous work shows that paracrine cytokines released by virus-infected human dendritic cells (DC) can dictate the maturation state of naïve DCs. To understand the effects of paracrine signaling, we systematically studied the effects of combinations cytokines in this complex mixture in generating an anti-viral state. After naïve DCs were exposed to either IFNβ or to paracrine signaling released by DCs infected by Newcastle disease virus (NDV), microarray analysis revealed a large number of genes that were differently regulated by the DC-secreted paracrine signaling. In order to identify the cytokine mechanisms involved, we identified 20 cytokines secreted by NDV infected DCs for which the corresponding receptor gene is expressed in naïve DCs. By exposing cells to all combinations of 19 cytokines (leave-one-out studies), we identified five cytokines (IFNβ, TNFα, IL-1β, TNFSF15, and IL28) as candidates for regulating DC maturation markers. Subsequent experiments identified IFNβ, TNFα, and IL1β as the major contributors to this anti-viral state. This finding was supported by infection studies in vitro, by T-cell activation studies and by in vivo infection studies in mouse. Combination of cytokines can cause response states in DCs that differ from those achieved by the individual cytokines alone. These results suggest that the cytokine microenvironment may act via a combinatorial code to direct the response state of specific immune cells. Further elucidation of this code may provide insight into responses to infection and neoplasia as well as guide the development of combinatorial cytokine immunomodulation for infectious, autoimmune, and immunosurveillance-related diseases.
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Affiliation(s)
- Boris M Hartmann
- Department of Neurology, Mount Sinai School of Medicine, Center for Translational Systems Biology , New York, NY , USA
| | - Nada Marjanovic
- Department of Neurology, Mount Sinai School of Medicine, Center for Translational Systems Biology , New York, NY , USA
| | - German Nudelman
- Department of Neurology, Mount Sinai School of Medicine, Center for Translational Systems Biology , New York, NY , USA
| | - Thomas M Moran
- Department of Microbiology, Mount Sinai School of Medicine, Center for Translational Systems Biology , New York, NY , USA
| | - Stuart C Sealfon
- Department of Neurology, Mount Sinai School of Medicine, Center for Translational Systems Biology , New York, NY , USA
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Tabbaa OP, Nudelman G, Sealfon SC, Hayot F, Jayaprakash C. Noise propagation through extracellular signaling leads to fluctuations in gene expression. BMC Syst Biol 2013; 7:94. [PMID: 24067165 PMCID: PMC3906959 DOI: 10.1186/1752-0509-7-94] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 09/17/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Cell-to-cell variability in mRNA and proteins has been observed in many biological systems, including the human innate immune response to viral infection. Most of these studies have focused on variability that arises from (a) intrinsic stochastic fluctuations in gene expression and (b) extrinsic sources (e.g. fluctuations in transcription factors). The main focus of our study is the effect of extracellular signaling on enhancing intrinsic stochastic fluctuations. As a new source of noise, the communication between cells with fluctuating numbers of components has received little attention. We use agent-based modeling to study this contribution to noise in a system of human dendritic cells responding to viral infection. RESULTS Our results, validated by single-cell experiments, show that in the transient state cell-to-cell variability in an interferon-stimulated gene (DDX58) arises from the interplay between the spatial randomness of the cellular sources of the interferon and the temporal stochasticity of its own production. The numerical simulations give insight into the time scales on which autocrine and paracrine signaling act in a heterogeneous population of dendritic cells upon viral infection. We study the effect of different factors that influence the magnitude of the cell-to-cell-variability of the induced gene, including the cell density, multiplicity of infection, and the time scale over which the cellular sources begin producing the cytokine. CONCLUSIONS We propose a mechanism of noise propagation through extracellular communication and establish conditions under which the mechanism is operative. The cellular stochasticity of gene induction, which we investigate, is not limited to the specific interferon-induced gene we have studied; a broad distribution of copy numbers across cells is to be expected for other interferon-stimulated genes. This can lead to functional consequences for the system-level response to a viral challenge.
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Affiliation(s)
- Omar P Tabbaa
- Department of Physics, Ohio State University, Columbus 43210, USA
| | - German Nudelman
- Department of Neurology, Mount Sinai School of Medicine, New York 10029, USA
| | - Stuart C Sealfon
- Department of Neurology, Mount Sinai School of Medicine, New York 10029, USA
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York 10029, USA
| | - Fernand Hayot
- Department of Neurology, Mount Sinai School of Medicine, New York 10029, USA
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York 10029, USA
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Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, Sealfon SC, Kleinstein SH. Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics 2013; 14 Suppl 6:S1. [PMID: 23734902 PMCID: PMC3633009 DOI: 10.1186/1471-2105-14-s6-s1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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] [Indexed: 12/15/2022] Open
Abstract
Background H1N1 influenza viruses were responsible for the 1918 pandemic that caused millions of deaths worldwide and the 2009 pandemic that caused approximately twenty thousand deaths. The cellular response to such virus infections involves extensive genetic reprogramming resulting in an antiviral state that is critical to infection control. Identifying the underlying transcriptional network driving these changes, and how this program is altered by virally-encoded immune antagonists, is a fundamental challenge in systems immunology. Results Genome-wide gene expression patterns were measured in human monocyte-derived dendritic cells (DCs) infected in vitro with seasonal H1N1 influenza A/New Caledonia/20/1999. To provide a mechanistic explanation for the timing of gene expression changes over the first 12 hours post-infection, we developed a statistically rigorous enrichment approach integrating genome-wide expression kinetics and time-dependent promoter analysis. Our approach, TIme-Dependent Activity Linker (TIDAL), generates a regulatory network that connects transcription factors associated with each temporal phase of the response into a coherent linked cascade. TIDAL infers 12 transcription factors and 32 regulatory connections that drive the antiviral response to influenza. To demonstrate the generality of this approach, TIDAL was also used to generate a network for the DC response to measles infection. The software implementation of TIDAL is freely available at http://tsb.mssm.edu/primeportal/?q=tidal_prog. Conclusions We apply TIDAL to reconstruct the transcriptional programs activated in monocyte-derived human dendritic cells in response to influenza and measles infections. The application of this time-centric network reconstruction method in each case produces a single transcriptional cascade that recapitulates the known biology of the response with high precision and recall, in addition to identifying potentially novel antiviral factors. The ability to reconstruct antiviral networks with TIDAL enables comparative analysis of antiviral responses, such as the differences between pandemic and seasonal influenza infections.
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Affiliation(s)
- Elena Zaslavsky
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA.
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Tabbaa OP, Nudelman G, Sealfon SC, Jayaprakash C. Noise Propagation through Cytokine Signaling Leads to Fluctuations in Interferon-Induced Genes. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Bar-On D, Wolter S, van de Linde S, Heilemann M, Nudelman G, Nachliel E, Gutman M, Sauer M, Ashery U. Super-resolution imaging reveals the internal architecture of nano-sized syntaxin clusters. J Biol Chem 2012; 287:27158-67. [PMID: 22700970 DOI: 10.1074/jbc.m112.353250] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Key synaptic proteins from the soluble SNARE (N-ethylmaleimide-sensitive factor attachment protein receptor) family, among many others, are organized at the plasma membrane of cells as clusters containing dozens to hundreds of protein copies. However, the exact membranal distribution of proteins into clusters or as single molecules, the organization of molecules inside the clusters, and the clustering mechanisms are unclear due to limitations of the imaging and analytical tools. Focusing on syntaxin 1 and SNAP-25, we implemented direct stochastic optical reconstruction microscopy together with quantitative clustering algorithms to demonstrate a novel approach to explore the distribution of clustered and nonclustered molecules at the membrane of PC12 cells with single-molecule precision. Direct stochastic optical reconstruction microscopy images reveal, for the first time, solitary syntaxin/SNAP-25 molecules and small clusters as well as larger clusters. The nonclustered syntaxin or SNAP-25 molecules are mostly concentrated in areas adjacent to their own clusters. In the clusters, the density of the molecules gradually decreases from the dense cluster core to the periphery. We further detected large clusters that contain several density gradients. This suggests that some of the clusters are formed by unification of several clusters that preserve their original organization or reorganize into a single unit. Although syntaxin and SNAP-25 share some common distributional features, their clusters differ markedly from each other. SNAP-25 clusters are significantly larger, more elliptical, and less dense. Finally, this study establishes methodological tools for the analysis of single-molecule-based super-resolution imaging data and paves the way for revealing new levels of membranal protein organization.
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Affiliation(s)
- Dana Bar-On
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
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Shimoni Y, Nudelman G, Hayot F, Sealfon SC. Multi-scale stochastic simulation of diffusion-coupled agents and its application to cell culture simulation. PLoS One 2011; 6:e29298. [PMID: 22216238 PMCID: PMC3244460 DOI: 10.1371/journal.pone.0029298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/23/2011] [Indexed: 11/18/2022] Open
Abstract
Many biological systems consist of multiple cells that interact by secretion and binding of diffusing molecules, thus coordinating responses across cells. Techniques for simulating systems coupling extracellular and intracellular processes are very limited. Here we present an efficient method to stochastically simulate diffusion processes, which at the same time allows synchronization between internal and external cellular conditions through a modification of Gillespie's chemical reaction algorithm. Individual cells are simulated as independent agents, and each cell accurately reacts to changes in its local environment affected by diffusing molecules. Such a simulation provides time-scale separation between the intra-cellular and extra-cellular processes. We use our methodology to study how human monocyte-derived dendritic cells alert neighboring cells about viral infection using diffusing interferon molecules. A subpopulation of the infected cells reacts early to the infection and secretes interferon into the extra-cellular medium, which helps activate other cells. Findings predicted by our simulation and confirmed by experimental results suggest that the early activation is largely independent of the fraction of infected cells and is thus both sensitive and robust. The concordance with the experimental results supports the value of our method for overcoming the challenges of accurately simulating multiscale biological signaling systems.
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Affiliation(s)
- Yishai Shimoni
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, New York, United States of America
- * E-mail: (YS); (GN)
| | - German Nudelman
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (YS); (GN)
| | - Fernand Hayot
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Stuart C. Sealfon
- Department of Neurology and Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
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Hu J, Nudelman G, Shimoni Y, Kumar M, Ding Y, López C, Hayot F, Wetmur JG, Sealfon SC. Role of cell-to-cell variability in activating a positive feedback antiviral response in human dendritic cells. PLoS One 2011; 6:e16614. [PMID: 21347441 PMCID: PMC3035661 DOI: 10.1371/journal.pone.0016614] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 01/03/2011] [Indexed: 12/22/2022] Open
Abstract
In the first few hours following Newcastle disease viral infection of human monocyte-derived dendritic cells, the induction of IFNB1 is extremely low and the secreted type I interferon response is below the limits of ELISA assay. However, many interferon-induced genes are activated at this time, for example DDX58 (RIGI), which in response to viral RNA induces IFNB1. We investigated whether the early induction of IFNBI in only a small percentage of infected cells leads to low level IFN secretion that then induces IFN-responsive genes in all cells. We developed an agent-based mathematical model to explore the IFNBI and DDX58 temporal dynamics. Simulations showed that a small number of early responder cells provide a mechanism for efficient and controlled activation of the DDX58-IFNBI positive feedback loop. The model predicted distributions of single cell responses that were confirmed by single cell mRNA measurements. The results suggest that large cell-to-cell variation plays an important role in the early innate immune response, and that the variability is essential for the efficient activation of the IFNB1 based feedback loop.
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Affiliation(s)
- Jianzhong Hu
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - German Nudelman
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Yishai Shimoni
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Madhu Kumar
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Yaomei Ding
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Carolina López
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Fernand Hayot
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - James G. Wetmur
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
- Center for Translational Systems Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Stuart C. Sealfon
- Department of Microbiology, Mount Sinai School of Medicine, New York, New York, United States of America
- Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
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Patil S, Pincas H, Seto J, Nudelman G, Nudelman I, Sealfon SC. Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. BMC Syst Biol 2010; 4:137. [PMID: 20929569 PMCID: PMC2958907 DOI: 10.1186/1752-0509-4-137] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 10/07/2010] [Indexed: 02/07/2023]
Abstract
Background Dendritic cells are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems. Much research has focused on the signaling pathways triggered upon infection of dendritic cells by various pathogens. The high level of activity in the field makes it desirable to have a pathway-based resource to access the information in the literature. Current pathway diagrams lack either comprehensiveness, or an open-access editorial interface. Hence, there is a need for a dependable, expertly curated knowledgebase that integrates this information into a map of signaling networks. Description We have built a detailed diagram of the dendritic cell signaling network, with the goal of providing researchers with a valuable resource and a facile method for community input. Network construction has relied on comprehensive review of the literature and regular updates. The diagram includes detailed depictions of pathways activated downstream of different pathogen recognition receptors such as Toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors and nucleotide-binding oligomerization domain-like receptors. Initially assembled using CellDesigner software, it provides an annotated graphical representation of interactions stored in Systems Biology Mark-up Language. The network, which comprises 249 nodes and 213 edges, has been web-published through the Biological Pathway Publisher software suite. Nodes are annotated with PubMed references and gene-related information, and linked to a public wiki, providing a discussion forum for updates and corrections. To gain more insight into regulatory patterns of dendritic cell signaling, we analyzed the network using graph-theory methods: bifan, feedforward and multi-input convergence motifs were enriched. This emphasis on activating control mechanisms is consonant with a network that subserves persistent and coordinated responses to pathogen detection. Conclusions This map represents a navigable aid for presenting a consensus view of the current knowledge on dendritic cell signaling that can be continuously improved through contributions of research community experts. Because the map is available in a machine readable format, it can be edited and may assist researchers in data analysis. Furthermore, the availability of a comprehensive knowledgebase might help further research in this area such as vaccine development. The dendritic cell signaling knowledgebase is accessible at http://tsb.mssm.edu/pathwayPublisher/DC_pathway/DC_pathway_index.html.
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Affiliation(s)
- Sonali Patil
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
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Fink MY, Pincas H, Choi SG, Nudelman G, Sealfon SC. Research resource: Gonadotropin-releasing hormone receptor-mediated signaling network in LbetaT2 cells: a pathway-based web-accessible knowledgebase. Mol Endocrinol 2010; 24:1863-71. [PMID: 20592162 DOI: 10.1210/me.2009-0530] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The GnRH receptor (GnRHR), expressed at the cell surface of the anterior pituitary gonadotrope, is critical for normal secretion of gonadotropins LH and FSH, pubertal development, and reproduction. The signaling network downstream of the GnRHR and the molecular bases of the regulation of gonadotropin expression have been the subject of intense research. The murine LbetaT2 cell line represents a mature gonadotrope and therefore is an important model for the study of GnRHR-signaling pathways and modulation of the gonadotrope cell by physiological regulators. In order to facilitate access to the information contained in this complex and evolving literature, we have developed a pathway-based knowledgebase that is web hosted. At present, using 106 relevant primary publications, we curated a comprehensive knowledgebase of the GnRHR signaling in the LbetaT2 cell in the form of a process diagram. Positive and negative controls of gonadotropin gene expression, which included GnRH itself, hypothalamic factors, gonadal steroids and peptides, as well as other hormones, were illustrated. The knowledgebase contains 187 entities and 206 reactions. It was assembled using CellDesigner software, which provides an annotated graphic representation of interactions, stored in Systems Biology Mark-up Language. We then utilized Biological Pathway Publisher, a software suite previously developed in our laboratory, to host the knowledgebase in a web-accessible format as a public resource. In addition, the network entities were linked to a public wiki, providing a forum for discussion, updating, and error correction. The GnRHR-signaling network is openly accessible at http://tsb.mssm.edu/pathwayPublisher/GnRHR_Pathway/GnRHR_Pathway_ index.html.
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Affiliation(s)
- Marc Y Fink
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
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Zablocki J, Palle V, Blackburn B, Elzein E, Nudelman G, Gothe S, Gao Z, Li Z, Meyer S, Belardinelli L. ChemInform Abstract: 2-Substituted Pi System Derivatives of Adenosine That Are Coronary Vasodilators Acting via the A2A Adenosine Receptor. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/chin.200147199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Nudelman G, Ge Y, Hu J, Kumar M, Seto J, Duke JL, Kleinstein SH, Hayot F, Sealfon SC, Wetmur JG. Coregulation mapping based on individual phenotypic variation in response to virus infection. Immunome Res 2010; 6:2. [PMID: 20298589 PMCID: PMC3161383 DOI: 10.1186/1745-7580-6-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 03/18/2010] [Indexed: 01/31/2023] Open
Abstract
Background Gene coregulation across a population is an important aspect of the considerable variability of the human immune response to virus infection. Methodology to investigate it must rely on a number of ingredients ranging from gene clustering to transcription factor enrichment analysis. Results We have developed a methodology to investigate the gene to gene correlations for the expression of 34 genes linked to the immune response of Newcastle Disease Virus (NDV) infected conventional dendritic cells (DCs) from 145 human donors. The levels of gene expression showed a large variation across individuals. We generated a map of gene co-expression using pairwise correlation and multidimensional scaling (MDS). The analysis of these data showed that among the 13 genes left after filtering for statistically significant variations, two clusters are formed. We investigated to what extent the observed correlation patterns can be explained by the sharing of transcription factors (TFs) controlling these genes. Our analysis showed that there was a significant positive correlation between MDS distances and TF sharing across all pairs of genes. We applied enrichment analysis to the TFs having binding sites in the promoter regions of those genes. This analysis, after Gene Ontology filtering, indicated the existence of two clusters of genes (CCL5, IFNA1, IFNA2, IFNB1) and (IKBKE, IL6, IRF7, MX1) that were transcriptionally co-regulated. In order to facilitate the use of our methodology by other researchers, we have also developed an interactive coregulation explorer web-based tool called CorEx. It permits the study of MDS and hierarchical clustering of data combined with TF enrichment analysis. We also offer web services that provide programmatic access to MDS, hierarchical clustering and TF enrichment analysis. Conclusions MDS mapping based on correlation in conjunction with TF enrichment analysis represents a useful computational method to generate predictions underlying gene coregulation across a population.
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Affiliation(s)
- German Nudelman
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Yongchao Ge
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Jianzhong Hu
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Madhu Kumar
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Jeremy Seto
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Jamie L Duke
- Interdepartmental Program in Computational Biology and Bioinformatics and Department of Pathology, Yale University, New Haven, Connecticut 06511, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics and Department of Pathology, Yale University, New Haven, Connecticut 06511, USA
| | - Fernand Hayot
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Stuart C Sealfon
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - James G Wetmur
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA
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Affiliation(s)
- Ganesh A Viswanathan
- Center for Translational Systems Biology and Department of Neurology, Mount Sinai School of Medicine, New York, New York, United States of America
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Abstract
B lymphocyte activation results from the stimulation by large immune complexes involving antigens, antibodies, rafts and complement factors. Cell activation requires co-localization of the interacting molecular components. One of the main elements leading to this localization is the presence on the cell surface of lipid rafts. We show here that an appropriate amount of lipid rafts help to significantly (2- 3 orders of magnitude) raise the sensitivity of B lymphocyte to surrounding high valence antigens. The analysis was done using a newly developed graphically visualized, Monte Carlo (MC) simulation of the cell surface dynamics. Currently this platform represents a feasible, advanced and reliable framework to investigate the cell surface in general. We describe the model and determine, utilizing our model, the effect of lipid rafts surface fraction on the properties of B cell response to immune complexes. We validate our results using an approximate set of ODEs.
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Affiliation(s)
- G Nudelman
- Fac. of Life Sci., Bar-Ilan Univ., Ramat-Gan, Israel
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Abstract
The cell membrane lies at the interface between an extracellular set of signals and the appropriate intracellular response. Specifically, lymphocyte activity is determined by the spatial and structural response to antigens, as mediated by cell surface receptors. In order to correlate experimentally observed cellular activities, such as secretion, anergy, death, survival and division to external stimuli, it is necessary to monitor cell surface dynamics. B-lymphocyte activation results from the stimulation by large immune complexes comprising antigens, B-cell receptors (BcRs) and co-receptors. Compartmentalisation of the interacting molecular components is required in order to assure the rapid initiation of specialised and sustained signalling cascades. In this study, a Monte Carlo simulation of the cell membrane dynamics was developed to clarify the receptor dynamics, aggregation mechanisms and their combined effect on cellular functions. This simulation is based on experimentally measured parameters and represents a feasible, advanced and reliable framework to investigate the cell surface. The current study focussed on B-cell surface dynamics. A model demonstrating the basic properties of BcR dynamics and how BcR kinetics is affected by lipid rafts is developed. The authors studied BcR interactions with multivalent ligands and the influence of lipid rafts on this interaction. Finally, the dynamics of the initial steps of BcR-mediated cell activation is estimated and the effect of the association of signalling molecules with lipid rafts is demonstrated. These results are used to suggest some novel hypotheses on BcR-mediated B-cell activation.
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Affiliation(s)
- G Nudelman
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Nudelman G, Tennenbaum T, Mehr R, Unger R. PESI--an intelligent system for prediction of enzyme-substrate interactions based on experimental constraints. In Silico Biol 2003; 2:495-505. [PMID: 12611629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
We present a system for predicting protein-protein modifications, and demonstrate its usefulness in the field of signal transduction research. Signal transduction is one of the most important areas of investigation in biological research. One of the major mechanisms frequently employed by cells to regulate signal transduction processes involves protein phosphorylation by various kinases. As many as 1,000 protein kinases and 500 protein phosphatases in the human genome are thought to be involved in phosphorylation processes which regulate all aspects of cell function. The complexity of such interactions stems from the enormous number of factors and interactions, which makes the identification of putative substrates for any given enzyme by straightforward experimentation increasingly difficult. We present here a data mining algorithm, based on the similarity between the modifier proteins and between the modified proteins, and on experimental constraints. The application presented here (PESI) focuses on substrate phosphorylation by various enzymes. This algorithm reduces the number of substrate candidates for experimental study by about two orders of magnitude. Moreover, this algorithm has already yielded predictions for previously unknown substrates of the enzymes PKCdelta and PKCeta, which we have confirmed experimentally.
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Affiliation(s)
- German Nudelman
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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