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Bateman NW, Abulez T, Soltis AR, McPherson A, Choi S, Garsed DW, Pandey A, Tian C, Hood BL, Conrads KA, Teng PN, Oliver J, Gist G, Mitchell D, Litzi TJ, Tarney CM, Crothers BA, Mhawech-Fauceglia P, Dalgard CL, Wilkerson MD, Pierobon M, Petricoin EF, Yan C, Meerzaman D, Bodelon C, Wentzensen N, Lee JSH, Huntsman DG, Shah S, Shriver CD, Phippen NT, Darcy KM, Bowtell DDL, Conrads TP, Maxwell GL. Author Correction: Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities. NPJ Precis Oncol 2024; 8:97. [PMID: 38710993 DOI: 10.1038/s41698-024-00588-9] [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: 05/08/2024] Open
Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrew McPherson
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Seongmin Choi
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Barbara A Crothers
- The Joint Pathology Center, Defense Health Agency, National Capital Region Medical Directorate, Silver Spring, MD, USA
| | - Paulette Mhawech-Fauceglia
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Jerry S H Lee
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab Shah
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Craig D Shriver
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
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Bateman NW, Abulez T, Soltis AR, McPherson A, Choi S, Garsed DW, Pandey A, Tian C, Hood BL, Conrads KA, Teng PN, Oliver J, Gist G, Mitchell D, Litzi TJ, Tarney CM, Crothers BA, Mhawech-Fauceglia P, Dalgard CL, Wilkerson MD, Pierobon M, Petricoin EF, Yan C, Meerzaman D, Bodelon C, Wentzensen N, Lee JSH, Huntsman DG, Shah S, Shriver CD, Phippen NT, Darcy KM, Bowtell DDL, Conrads TP, Maxwell GL. Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities. NPJ Precis Oncol 2024; 8:68. [PMID: 38480868 PMCID: PMC10937683 DOI: 10.1038/s41698-024-00519-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/15/2024] [Indexed: 03/17/2024] Open
Abstract
We performed a deep proteogenomic analysis of bulk tumor and laser microdissection enriched tumor cell populations from high-grade serous ovarian cancer (HGSOC) tissue specimens spanning a broad spectrum of purity. We identified patients with longer progression-free survival had increased immune-related signatures and validated proteins correlating with tumor-infiltrating lymphocytes in 65 tumors from an independent cohort of HGSOC patients, as well as with overall survival in an additional 126 HGSOC patient cohort. We identified that homologous recombination deficient (HRD) tumors are enriched in pathways associated with metabolism and oxidative phosphorylation that we validated in independent patient cohorts. We further identified that polycomb complex protein BMI-1 is elevated in HR proficient (HRP) tumors, that elevated BMI-1 correlates with poor overall survival in HRP but not HRD HGSOC patients, and that HRP HGSOC cells are uniquely sensitive to BMI-1 inhibition.
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Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrew McPherson
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Seongmin Choi
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Barbara A Crothers
- The Joint Pathology Center, Defense Health Agency, National Capital Region Medical Directorate, Silver Spring, MD, USA
| | - Paulette Mhawech-Fauceglia
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Jerry S H Lee
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab Shah
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Craig D Shriver
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
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Slaven JE, Wilkerson M, Soltis AR, Rittase WB, Bradfield DT, Bylicky M, Cary L, Tsioplaya A, Bouten R, Dalgard C, Day RM. Transcriptomic Profiling and Pathway Analysis of Mesenchymal Stem Cells Following Low Dose-Rate Radiation Exposure. Antioxidants (Basel) 2023; 12:antiox12020241. [PMID: 36829800 PMCID: PMC9951969 DOI: 10.3390/antiox12020241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Low dose-rate radiation exposure can occur in medical imaging, as background from environmental or industrial radiation, and is a hazard of space travel. In contrast with high dose-rate radiation exposure that can induce acute life-threatening syndromes, chronic low-dose radiation is associated with Chronic Radiation Syndrome (CRS), which can alter environmental sensitivity. Secondary effects of chronic low dose-rate radiation exposure include circulatory, digestive, cardiovascular, and neurological diseases, as well as cancer. Here, we investigated 1-2 Gy, 0.66 cGy/h, 60Co radiation effects on primary human mesenchymal stem cells (hMSC). There was no significant induction of apoptosis or DNA damage, and cells continued to proliferate. Gene ontology (GO) analysis of transcriptome changes revealed alterations in pathways related to cellular metabolism (cholesterol, fatty acid, and glucose metabolism), extracellular matrix modification and cell adhesion/migration, and regulation of vasoconstriction and inflammation. Interestingly, there was increased hypoxia signaling and increased activation of pathways regulated by iron deficiency, but Nrf2 and related genes were reduced. The data were validated in hMSC and human lung microvascular endothelial cells using targeted qPCR and Western blotting. Notably absent in the GO analysis were alteration pathways for DNA damage response, cell cycle inhibition, senescence, and pro-inflammatory response that we previously observed for high dose-rate radiation exposure. Our findings suggest that cellular gene transcription response to low dose-rate ionizing radiation is fundamentally different compared to high-dose-rate exposure. We hypothesize that cellular response to hypoxia and iron deficiency are driving processes, upstream of the other pathway regulation.
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Affiliation(s)
- John E. Slaven
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Matthew Wilkerson
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Anthony R. Soltis
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - W. Bradley Rittase
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Dmitry T. Bradfield
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Michelle Bylicky
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Lynnette Cary
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Alena Tsioplaya
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Roxane Bouten
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
| | - Clifton Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Regina M. Day
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA
- Correspondence: ; Tel.: +1-301-295-3236; Fax: +1-301-295-3220
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Lippa SM, Lange RT, Dalgard CL, Soltis AR, Guedes VA, Brickell TA, French LM, Gill J. APOE Is Associated With Serum Tau Following Uncomplicated Mild Traumatic Brain Injury. Front Neurol 2022; 13:816625. [PMID: 35911887 PMCID: PMC9329522 DOI: 10.3389/fneur.2022.816625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Objectives APOE e4 has been linked to poor outcome following traumatic brain injury (TBI); however, the mechanisms behind this relationship are unclear. Few studies have investigated the relationship between the APOE genotype and established brain related protein biomarkers following TBI. The purpose of this study was to examine this relationship in service members and veterans (SMVs) following TBI. Methods Participants were 209 SMVs [124 uncomplicated mild TBI (mTBI); 85 complicated mild, moderate, severe, or penetrating TBI (mod-sev TBI)] prospectively enrolled in the DVBIC-TBICoE 15-Year Longitudinal TBI Study. APOE genotyping was undertaken using non-fasting blood serum samples. Participants were divided into three groups: APOE e2+, APOE e3/e3, and APOE e4+. Results In participants with mTBI, those with the APOE e2 allele had significantly lower levels of tau than those with APOE e4 (p = 0.005, r = 0.43, medium-large effect size). Those with APOE e3/e3 trended toward having higher tau than those APOE e2+ (p = 0.076, r = 0.20, small-medium effect size) and lower tau than those with APOE e4+ (p = 0.062, r = 0.21, small-medium effect size). There were no significant differences in biomarkers based on APOE in the mod-sev TBI group. Discussion This study is the first to demonstrate APOE genotype is related to serum tau levels following a mTBI, extending prior findings to human serum following mTBI. In addition to higher serum tau levels in APOE e4 carriers, lower tau levels were observed in APOE e2 carriers, suggesting a possible protective effect.
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Affiliation(s)
- Sara M. Lippa
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Rael T. Lange
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
- Department of Research, Tramatic Brain Injury Center of Excellence, Silver Spring, MD, United States
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
- Centre of Excellence on Post-traumatic Stress Disorder, Ottawa, ON, Canada
- General Dynamics Information Technology, Falls Church, VA, United States
| | - Clifton L. Dalgard
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- The American Genome Center, Bethesda, MD, United States
| | - Anthony R. Soltis
- Henry M. Jackson Foundation, Bethesda, MD, United States
- PRIMER, Bethesda, MD, United States
| | | | - Tracey A. Brickell
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
- Department of Research, Tramatic Brain Injury Center of Excellence, Silver Spring, MD, United States
- Centre of Excellence on Post-traumatic Stress Disorder, Ottawa, ON, Canada
- General Dynamics Information Technology, Falls Church, VA, United States
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Louis M. French
- National Intrepid Center of Excellence, Walter Reed National Military Medical Center, Bethesda, MD, United States
- Department of Research, Tramatic Brain Injury Center of Excellence, Silver Spring, MD, United States
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Jessica Gill
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
- School of Nursing, Johns Hopkins University, Baltimore, MD, United States
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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Nguyen N, Gudmundsson KO, Soltis AR, Oakley K, Roy KR, Han Y, Gurnari C, Maciejewski JP, Crouch G, Ernst P, Dalgard CL, Du Y. Recruitment of MLL1 complex is essential for SETBP1 to induce myeloid transformation. iScience 2022; 25:103679. [PMID: 35036869 PMCID: PMC8749219 DOI: 10.1016/j.isci.2021.103679] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/26/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Abnormal activation of SETBP1 due to overexpression or missense mutations occurs frequently in various myeloid neoplasms and associates with poor prognosis. Direct activation of Hoxa9/Hoxa10/Myb transcription by SETBP1 and its missense mutants is essential for their transforming capability; however, the underlying epigenetic mechanisms remain elusive. We found that both SETBP1 and its missense mutant SETBP1(D/N) directly interact with histone methyltransferase MLL1. Using a combination of ChIP-seq and RNA-seq analysis in primary hematopoietic stem and progenitor cells, we uncovered extensive overlap in their genomic occupancy and their cooperation in activating many oncogenic transcription factor genes including Hoxa9/Hoxa10/Myb and a large group of ribosomal protein genes. Genetic ablation of Mll1 as well as treatment with an inhibitor of the MLL1 complex OICR-9429 abrogated Setbp1/Setbp1(D/N)-induced transcriptional activation and transformation. Thus, the MLL1 complex plays a critical role in Setbp1-induced transcriptional activation and transformation and represents a promising target for treating myeloid neoplasms with SETBP1 activation.
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Affiliation(s)
- Nhu Nguyen
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Kristbjorn O. Gudmundsson
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Anthony R. Soltis
- The American Genome Center (TAGC), Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Kevin Oakley
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Kartik R. Roy
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Yufen Han
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gary Crouch
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Patricia Ernst
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Clifton L. Dalgard
- The American Genome Center (TAGC), Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Yang Du
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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Hupalo D, Forsberg CW, Goldberg J, Kremen WS, Lyons MJ, Soltis AR, Viollet C, Ursano RJ, Stein MB, Franz CE, Sun YV, Vaccarino V, Smith NL, Dalgard CL, Wilkerson MD, Pollard HB. Rare variant association study of veteran twin whole-genomes links severe depression with a nonsynonymous change in the neuronal gene BHLHE22. World J Biol Psychiatry 2022; 23:295-306. [PMID: 34664540 PMCID: PMC9148382 DOI: 10.1080/15622975.2021.1980316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep whole-genome sequencing data in an independent population. METHODS We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according to DSM-III-R diagnostic criteria. Searching only rare variants in genomic regions from recent GWAS on MDD, we used the optimised sequence kernel association test and Fisher's Exact test to fine map loci associated with severe depression. RESULTS Our analysis identified one gene associated with severe depression, basic helix loop helix e22 (PAdjusted = 0.03) via SKAT-O test between unrelated severely depressed cases compared to unrelated non-depressed controls. The same gene BHLHE22 had a non-silent variant rs13279074 (PAdjusted = 0.032) based on a single variant Fisher's Exact test between unrelated severely depressed cases compared to unrelated non-depressed controls. CONCLUSION The gene BHLHE22 shows compelling genetic evidence of directly impacting the severe depression phenotype. Together these results advance understanding of the genetic contribution to major depressive disorder in a new cohort and link a rare variant to severe forms of the disorder.
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Affiliation(s)
- Daniel Hupalo
- The American Genome Center, Collaborative Health Initiative Research Program, and Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Christopher W. Forsberg
- Seattle Epidemiologic Research and Information Center, Office of Research and Development, U.S. Department of Veteran Affairs, Seattle, WA, USA
| | - Jack Goldberg
- Seattle Epidemiologic Research and Information Center, Office of Research and Development, U.S. Department of Veteran Affairs, Seattle, WA, USA;,Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - William S. Kremen
- Department of Psychiatry and of Family Medicine & Public Health, University of California, La Jolla, CA, USA;,VA San Diego Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Michael J. Lyons
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
| | - Anthony R. Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, and Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Coralie Viollet
- The American Genome Center, Collaborative Health Initiative Research Program, and Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Robert J. Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Murray B. Stein
- Department of Psychiatry and of Family Medicine & Public Health, University of California, La Jolla, CA, USA
| | - Carol E. Franz
- Department of Psychiatry and of Family Medicine & Public Health, University of California, La Jolla, CA, USA
| | - Yan V. Sun
- Department of Epidemiology, Emory University, Atlanta, GA, USA
| | - Viola Vaccarino
- Department of Epidemiology, Emory University, Atlanta, GA, USA
| | - Nicholas L. Smith
- Seattle Epidemiologic Research and Information Center, Office of Research and Development, U.S. Department of Veteran Affairs, Seattle, WA, USA;,Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Clifton L. Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, and Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA;,Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Matthew D. Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, and Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA;,Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Harvey B. Pollard
- The American Genome Center, Collaborative Health Initiative Research Program, and Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA;,Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, USA
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7
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Bateman NW, Tarney CM, Abulez TS, Hood BL, Conrads KA, Zhou M, Soltis AR, Teng PN, Jackson A, Tian C, Dalgard CL, Wilkerson MD, Kessler MD, Goecker Z, Loffredo J, Shriver CD, Hu H, Cote M, Parker GJ, Segars J, Al-Hendy A, Risinger JI, Phippen NT, Casablanca Y, Darcy KM, Maxwell GL, Conrads TP, O'Connor TD. Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry. iScience 2021; 25:103665. [PMID: 35036865 PMCID: PMC8753123 DOI: 10.1016/j.isci.2021.103665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/29/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
Characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step to connect patient ancestry with disease pathogenesis. Nonsynonymous single-nucleotide polymorphisms encoding missense substitutions within tryptic peptides exhibiting high allele frequencies in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs), were prioritized from 1000 genomes. In silico analysis identified that as few as 20 pAIMs can determine ancestry proportions similarly to >260K SNPs (R2 = 0.99). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma tissues combined resulted in the quantitation of 62 pAIMs that correlate with patient race and genotype-confirmed ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. pAIMs will support generalized proteoancestry assessment as well as efforts investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms.
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Affiliation(s)
- Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,Corresponding author 3289 Woodburn Rd, Suite 375, Annandale, VA 22003;
| | - Christopher M. Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Tamara S. Abulez
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Brian L. Hood
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Kelly A. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Ming Zhou
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Anthony R. Soltis
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Amanda Jackson
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Clifton L. Dalgard
- The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA,Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D. Wilkerson
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA,Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Michael D. Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zachary Goecker
- University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeremy Loffredo
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Craig D. Shriver
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Hai Hu
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | | | - Glendon J. Parker
- University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - James Segars
- Johns Hopkins University Medical Center, Baltimore, MD 21218, USA
| | - Ayman Al-Hendy
- The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - John I. Risinger
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI 48824, USA
| | - Neil T. Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - G. Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA,Program in Personalize and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA,Marlene and Stewart Greenebaum Comprehensive Cancer, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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8
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McCormack NM, Villalón E, Viollet C, Soltis AR, Dalgard CL, Lorson CL, Burnett BG. Survival motor neuron deficiency slows myoblast fusion through reduced myomaker and myomixer expression. J Cachexia Sarcopenia Muscle 2021; 12:1098-1116. [PMID: 34115448 PMCID: PMC8350220 DOI: 10.1002/jcsm.12740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 05/05/2021] [Accepted: 05/21/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Spinal muscular atrophy is an inherited neurodegenerative disease caused by insufficient levels of the survival motor neuron (SMN) protein. Recently approved treatments aimed at increasing SMN protein levels have dramatically improved patient survival and have altered the disease landscape. While restoring SMN levels slows motor neuron loss, many patients continue to have smaller muscles and do not achieve normal motor milestones. While timing of treatment is important, it remains unclear why SMN restoration is insufficient to fully restore muscle size and function. We and others have shown that SMN-deficient muscle precursor cells fail to efficiently fuse into myotubes. However, the role of SMN in myoblast fusion is not known. METHODS In this study, we show that SMN-deficient myoblasts readily fuse with wild-type myoblasts, demonstrating fusion competency. Conditioned media from wild type differentiating myoblasts do not rescue the fusion deficit of SMN-deficient cells, suggesting that compromised fusion may primarily be a result of altered membrane dynamics at the cell surface. Transcriptome profiling of skeletal muscle from SMN-deficient mice revealed altered expression of cell surface fusion molecules. Finally, using cell and mouse models, we investigate if myoblast fusion can be rescued in SMN-deficient myoblast and improve the muscle pathology in SMA mice. RESULTS We found reduced expression of the muscle fusion proteins myomaker (P = 0.0060) and myomixer (P = 0.0051) in the muscle of SMA mice. Suppressing SMN expression in C2C12 myoblast cells reduces expression of myomaker (35% reduction; P < 0.0001) and myomixer, also known as myomerger and minion, (30% reduction; P < 0.0001) and restoring SMN levels only partially restores myomaker and myomixer expression. Ectopic expression of myomixer improves myofibre number (55% increase; P = 0.0006) and motor function (35% decrease in righting time; P = 0.0089) in SMA model mice and enhances motor function (82% decrease in righting time; P < 0.0001) and extends survival (28% increase; P < 0.01) when administered in combination with an antisense oligonucleotide that increases SMN protein levels. CONCLUSIONS Here, we identified reduced expression of muscle fusion proteins as a key factor in the fusion deficits of SMN-deficient myoblasts. This discovery provides a novel target to improve SMA muscle pathology and motor function, which in combination with SMN increasing therapy could enhance clinical outcomes for SMA patients.
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Affiliation(s)
- Nikki M McCormack
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD, USA
| | - Eric Villalón
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Coralie Viollet
- Collaborative Health Initiative Research Program, Uniformed Services University of the Heath Sciences, Bethesda, MD, USA
| | - Anthony R Soltis
- Collaborative Health Initiative Research Program, Uniformed Services University of the Heath Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD, USA.,Collaborative Health Initiative Research Program, Uniformed Services University of the Heath Sciences, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Barrington G Burnett
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Bethesda, MD, USA
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9
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Lange RT, Merritt VC, Brickell TA, Dalgard CL, Soltis AR, Hershaw J, Lippa SM, Gill J, French LM. Apolipoprotein E e4 is associated with worse self-reported neurobehavioral symptoms following uncomplicated mild traumatic brain injury in U.S. military service members. Behav Brain Res 2021; 415:113491. [PMID: 34333069 DOI: 10.1016/j.bbr.2021.113491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/24/2021] [Accepted: 07/25/2021] [Indexed: 11/16/2022]
Abstract
Past research has found a relationship between the apolipoprotein E (APOE) e4 allele and worse neurobehavioral functioning following mild traumatic brain injury (MTBI) in civilian populations. The purpose of this study was to examine this relationship in service members and veterans (SMVs) following MTBI. Participants were 151 SMVs (103 uncomplicated MTBI; 48 Injured Controls [IC]) prospectively enrolled in the DVBIC-TBICoE 15-Year Longitudinal TBI Study. Participants completed a battery of self-reported neurobehavioral symptom measures on average 76.2 months post-injury (SD = 31.8). APOE genotyping was undertaken using non-fasting blood samples. Participants were classified into four subgroups based on injury (MTBI vs. IC) and APOE e4 allele status (e4 present/absent). In the IC group, there were no significant differences across APOE e4 status subgroups for all measures. In the MTBI group, participants with the APOE e4 allele had significantly worse scores on measures of depression, pain, anxiety, grief, positive well-being, social participation, and resilience compared to those without the e4 allele (d = .44 to d = .69). When comparing the number of 'clinically elevated' neurobehavioral measures simultaneously, the MTBI/e4 present subgroup consistently had a higher number of elevated measures compared to the MTBI/e4 absent, IC/e4 present, and IC/e4 absent subgroups. The APOE e4 allele was associated with poorer neurobehavioral outcome in SMVs in the chronic phase of recovery following MTBI. APOE e4 could be incorporated into screening tools to predict SMVs at risk for poor long-term neurobehavioral outcome in an effort to provide early intervention to improve long-term clinical outcome.
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Affiliation(s)
- Rael T Lange
- Traumatic Brain Injury Center of Excellence, 1335 E W Hwy, Silver Spring, MD, 20910, United States; Walter Reed National Military Medical Center, 4494 Palmer Rd N, Bethesda, MD, 20814, United States; National Intrepid Center of Excellence, Palmer Rd S, Bethesda, MD, 20814, United States; University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Contractor, General Dynamics Information Technology, 3150 Fairview Park Dr, Falls Church, VA, 22042, United States; Centre of Excellence on Post-traumatic Stress Disorder, 1145 Carling Ave, Ottawa, ON, K1Z 7K4, Canada.
| | - Victoria C Merritt
- VA San Diego Healthcare System, 3350 La Jolla Village Dr, San Diego, CA, 92161, United States; University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States.
| | - Tracey A Brickell
- Traumatic Brain Injury Center of Excellence, 1335 E W Hwy, Silver Spring, MD, 20910, United States; Walter Reed National Military Medical Center, 4494 Palmer Rd N, Bethesda, MD, 20814, United States; National Intrepid Center of Excellence, Palmer Rd S, Bethesda, MD, 20814, United States; Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD, 20814, United States; Contractor, General Dynamics Information Technology, 3150 Fairview Park Dr, Falls Church, VA, 22042, United States; Centre of Excellence on Post-traumatic Stress Disorder, 1145 Carling Ave, Ottawa, ON, K1Z 7K4, Canada.
| | - Clifton L Dalgard
- Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD, 20814, United States; The American Genome Center, 4301 Jones Bridge Rd, Bethesda, MD, 20814, United States.
| | - Anthony R Soltis
- Henry M Jackson Foundation, 6720A Rockledge Dr, Bethesda, MD, 20817, United States; PRIMER, 4301 Jones Bridge Rd, Bethesda, MD, 20814, United States.
| | - Jamie Hershaw
- Traumatic Brain Injury Center of Excellence, 1335 E W Hwy, Silver Spring, MD, 20910, United States; Walter Reed National Military Medical Center, 4494 Palmer Rd N, Bethesda, MD, 20814, United States; National Intrepid Center of Excellence, Palmer Rd S, Bethesda, MD, 20814, United States; Contractor, General Dynamics Information Technology, 3150 Fairview Park Dr, Falls Church, VA, 22042, United States.
| | - Sara M Lippa
- Walter Reed National Military Medical Center, 4494 Palmer Rd N, Bethesda, MD, 20814, United States; National Intrepid Center of Excellence, Palmer Rd S, Bethesda, MD, 20814, United States.
| | - Jessica Gill
- National Institutes of Health, National Institute of Nursing Research, 10 Center Dr, Bethesda, MD, 20814, United States.
| | - Louis M French
- Traumatic Brain Injury Center of Excellence, 1335 E W Hwy, Silver Spring, MD, 20910, United States; Walter Reed National Military Medical Center, 4494 Palmer Rd N, Bethesda, MD, 20814, United States; National Intrepid Center of Excellence, Palmer Rd S, Bethesda, MD, 20814, United States; Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD, 20814, United States.
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10
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Bandres-Ciga S, Saez-Atienzar S, Kim JJ, Makarious MB, Faghri F, Diez-Fairen M, Iwaki H, Leonard H, Botia J, Ryten M, Hernandez D, Gibbs JR, Ding J, Gan-Or Z, Noyce A, Pihlstrom L, Torkamani A, Soltis AR, Dalgard CL, Scholz SW, Traynor BJ, Ehrlich D, Scherzer CR, Bookman M, Cookson M, Blauwendraat C, Nalls MA, Singleton AB. Correction to: Large‑scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease. Acta Neuropathol 2021; 142:223-224. [PMID: 33944973 PMCID: PMC8496667 DOI: 10.1007/s00401-021-02309-z] [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] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A correction to this paper has been published: https://doi.org/10.1007/s00401-021-02309-z
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Affiliation(s)
- S Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - S Saez-Atienzar
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J J Kim
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M B Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - F Faghri
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M Diez-Fairen
- Fundació Docència i Recerca Mútua Terrassa and Movement Disorders Unit, Department of Neurology, University Hospital Mútua Terrassa, Terrassa, 08221, Barcelona, Spain
| | - H Iwaki
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - H Leonard
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - M Ryten
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - D Hernandez
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J R Gibbs
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J Ding
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Z Gan-Or
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - A Noyce
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London and Department of Neurology, Royal London Hospital, London, UK
| | - L Pihlstrom
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - A Torkamani
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - A R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MA, USA
| | - C L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MA, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MA, USA
| | - S W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, 21287, USA
| | - B J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, 21287, USA
| | - D Ehrlich
- Parkinson's Disease Clinic, Office of the Clinical Director, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - C R Scherzer
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 0115, USA
| | - M Bookman
- Verily Life Sciences, South San Francisco, CA, USA
| | - M Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MA, USA
| | - C Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M A Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Data Tecnica International, Glen Echo, MD, 20812, USA
| | - A B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.
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11
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Walton NI, Zhang X, Soltis AR, Starr J, Dalgard CL, Wilkerson MD, Conrad D, Pollard HB. Tensin 1 (TNS1) is a modifier gene for low body mass index (BMI) in homozygous [F508del]CFTR patients. Physiol Rep 2021; 9:e14886. [PMID: 34086412 PMCID: PMC8176904 DOI: 10.14814/phy2.14886] [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: 04/08/2021] [Accepted: 05/02/2021] [Indexed: 11/24/2022] Open
Abstract
Cystic fibrosis (CF) is a life‐limiting autosomal recessive genetic disease caused by variants in the CFTR gene, most commonly by the [F508del] variant. Although CF is a classical Mendelian disease, genetic variants in several modifier genes have been associated with variation of the clinical phenotype for pulmonary and gastrointestinal function and urogenital development. We hypothesized that whole genome sequencing of a well‐phenotyped CF populations might identify novel variants in known, or hitherto unknown, modifier genes. Whole genome sequencing was performed on the Illumina HiSeq X platform for 98 clinically diagnosed cystic fibrosis patient samples from the Adult CF Clinic at the University of California San Diego (UCSD). We compared protein‐coding, non‐silent variants genome wide between CFTR [F508del] homozygotes vs CFTR compound heterozygotes. Based on a single variant score test, we found 3 SNPs in common variants (MAF >5%) that occurred at significantly different rates between homozygous [F508del]CFTR and compound heterozygous [F508del]CFTR patients. The 3 SNPs were all located in one gene on chromosome 2: Tensin 1 (TNS1: rs3796028; rs2571445: and rs918949). We observed significantly lower BMIs in homozygous [F508del]CFTR patients who were also homozygous for Tensin 1 rs918949 (T/T) (p = 0.023) or rs2571445 (G/G) (p = 0.02) variants. The Tensin 1 gene is thus a potential modifier gene for low BMI in CF patients homozygous for the [F508del]CFTR variant.
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Affiliation(s)
- Nathan I Walton
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Consortium for Health and Military Performance, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Xijun Zhang
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Anthony R Soltis
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Joshua Starr
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Douglas Conrad
- Department of Medicine, University of California, San Diego, CA, USA
| | - Harvey B Pollard
- The Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Consortium for Health and Military Performance, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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12
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Dillon LW, Ghannam J, Nosiri C, Gui G, Goswami M, Calvo KR, Lindblad KE, Oetjen KA, Wilkerson M, Soltis AR, Sukumar G, Dalgard CL, Thompson J, Valdez J, DeStefano CB, Lai C, Sciambi A, Durruthy-Durruthy R, Llanso A, Gulati S, Wang S, Ooi A, Dagur PK, McCoy JP, Burr P, Li Y, Hourigan CS. Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Non-Malignant Clonal Hematopoiesis. Blood Cancer Discov 2021; 2:319-325. [PMID: 34258102 DOI: 10.1158/2643-3230.bcd-21-0046] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Genetic mutations associated with acute myeloid leukemia (AML) also occur in age-related clonal hematopoiesis, often in the same individual. This makes confident assignment of detected variants to malignancy challenging. The issue is particularly crucial for AML post-treatment measurable residual disease monitoring, where results can be discordant between genetic sequencing and flow cytometry. We show here, that it is possible to distinguish AML from clonal hematopoiesis and to resolve the immunophenotypic identity of clonal architecture. To achieve this, we first design patient-specific DNA probes based on patient's whole-genome sequencing, and then use them for patient-personalized single-cell DNA sequencing with simultaneous single-cell antibody-oligonucleotide sequencing. Examples illustrate AML arising from DNMT3A and TET2 mutated clones as well as independently. The ability to personalize single-cell proteogenomic assessment for individual patients based on leukemia-specific genomic features has implications for ongoing AML precision medicine efforts.
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Affiliation(s)
- Laura W Dillon
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Jack Ghannam
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Chidera Nosiri
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Gege Gui
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Meghali Goswami
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Katherine R Calvo
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892 United States
| | - Katherine E Lindblad
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Karolyn A Oetjen
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Matthew Wilkerson
- Precision Medicine Initiative for Military Medical Research and Education, Uniformed Services University of the Health Sciences, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD 20817.,Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Anthony R Soltis
- Precision Medicine Initiative for Military Medical Research and Education, Uniformed Services University of the Health Sciences, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD 20817
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD 20817.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Julie Thompson
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Janet Valdez
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Christin B DeStefano
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Catherine Lai
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Adam Sciambi
- Mission Bio, Inc., South San Francisco, CA, 94080, USA
| | | | - Aaron Llanso
- Mission Bio, Inc., South San Francisco, CA, 94080, USA
| | | | - Shu Wang
- Mission Bio, Inc., South San Francisco, CA, 94080, USA
| | - Aik Ooi
- Mission Bio, Inc., South San Francisco, CA, 94080, USA
| | - Pradeep K Dagur
- Flow Cytometry Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - J Philip McCoy
- Flow Cytometry Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Patrick Burr
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Yuesheng Li
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 United States
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13
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Attilio PJ, Snapper DM, Rusnak M, Isaac A, Soltis AR, Wilkerson MD, Dalgard CL, Symes AJ. Transcriptomic Analysis of Mouse Brain After Traumatic Brain Injury Reveals That the Angiotensin Receptor Blocker Candesartan Acts Through Novel Pathways. Front Neurosci 2021; 15:636259. [PMID: 33828448 PMCID: PMC8019829 DOI: 10.3389/fnins.2021.636259] [Citation(s) in RCA: 4] [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: 12/01/2020] [Accepted: 02/19/2021] [Indexed: 12/30/2022] Open
Abstract
Traumatic brain injury (TBI) results in complex pathological reactions, where the initial lesion is followed by secondary inflammation and edema. Our laboratory and others have reported that angiotensin receptor blockers (ARBs) have efficacy in improving recovery from traumatic brain injury in mice. Treatment of mice with a subhypotensive dose of the ARB candesartan results in improved functional recovery, and reduced pathology (lesion volume, inflammation and gliosis). In order to gain a better understanding of the molecular mechanisms through which candesartan improves recovery after controlled cortical impact injury (CCI), we performed transcriptomic profiling on brain regions after injury and drug treatment. We examined RNA expression in the ipsilateral hippocampus, thalamus and hypothalamus at 3 or 29 days post injury (dpi) treated with either candesartan (0.1 mg/kg) or vehicle. RNA was isolated and analyzed by bulk mRNA-seq. Gene expression in injured and/or candesartan treated brain region was compared to that in sham vehicle treated mice in the same brain region to identify genes that were differentially expressed (DEGs) between groups. The most DEGs were expressed in the hippocampus at 3 dpi, and the number of DEGs reduced with distance and time from the lesion. Among pathways that were differentially expressed at 3 dpi after CCI, candesartan treatment altered genes involved in angiogenesis, interferon signaling, extracellular matrix regulation including integrins and chromosome maintenance and DNA replication. At 29 dpi, candesartan treatment reduced the expression of genes involved in the inflammatory response. Some changes in gene expression were confirmed in a separate cohort of animals by qPCR. Fewer DEGs were found in the thalamus, and only one in the hypothalamus at 3 dpi. Additionally, in the hippocampi of sham injured mice, 3 days of candesartan treatment led to the differential expression of 384 genes showing that candesartan in the absence of injury had a powerful impact on gene expression specifically in the hippocampus. Our results suggest that candesartan has broad actions in the brain after injury and affects different processes at acute and chronic times after injury. These data should assist in elucidating the beneficial effect of candesartan on recovery from TBI.
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Affiliation(s)
- Peter J. Attilio
- Graduate Program in Neuroscience, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Dustin M. Snapper
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Milan Rusnak
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Akira Isaac
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Anthony R. Soltis
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Matthew D. Wilkerson
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Aviva J. Symes
- Graduate Program in Neuroscience, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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14
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Bandres-Ciga S, Saez-Atienzar S, Kim JJ, Makarious MB, Faghri F, Diez-Fairen M, Iwaki H, Leonard H, Botia J, Ryten M, Hernandez D, Gibbs JR, Ding J, Gan-Or Z, Noyce A, Pihlstrom L, Torkamani A, Soltis AR, Dalgard CL, Scholz SW, Traynor BJ, Ehrlich D, Scherzer CR, Bookman M, Cookson M, Blauwendraat C, Nalls MA, Singleton AB. Large-scale pathway specific polygenic risk and transcriptomic community network analysis identifies novel functional pathways in Parkinson disease. Acta Neuropathol 2020; 140:341-358. [PMID: 32601912 PMCID: PMC8096770 DOI: 10.1007/s00401-020-02181-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 05/05/2020] [Revised: 06/07/2020] [Accepted: 06/14/2020] [Indexed: 01/21/2023]
Abstract
Polygenic inheritance plays a central role in Parkinson disease (PD). A priority in elucidating PD etiology lies in defining the biological basis of genetic risk. Unraveling how risk leads to disruption will yield disease-modifying therapeutic targets that may be effective. Here, we utilized a high-throughput and hypothesis-free approach to determine biological processes underlying PD using the largest currently available cohorts of genetic and gene expression data from International Parkinson's Disease Genetics Consortium (IPDGC) and the Accelerating Medicines Partnership-Parkinson's disease initiative (AMP-PD), among other sources. We applied large-scale gene-set specific polygenic risk score (PRS) analyses to assess the role of common variation on PD risk focusing on publicly annotated gene sets representative of curated pathways. We nominated specific molecular sub-processes underlying protein misfolding and aggregation, post-translational protein modification, immune response, membrane and intracellular trafficking, lipid and vitamin metabolism, synaptic transmission, endosomal-lysosomal dysfunction, chromatin remodeling and apoptosis mediated by caspases among the main contributors to PD etiology. We assessed the impact of rare variation on PD risk in an independent cohort of whole-genome sequencing data and found evidence for a burden of rare damaging alleles in a range of processes, including neuronal transmission-related pathways and immune response. We explored enrichment linked to expression cell specificity patterns using single-cell gene expression data and demonstrated a significant risk pattern for dopaminergic neurons, serotonergic neurons, hypothalamic GABAergic neurons, and neural progenitors. Subsequently, we created a novel way of building de novo pathways by constructing a network expression community map using transcriptomic data derived from the blood of PD patients, which revealed functional enrichment in inflammatory signaling pathways, cell death machinery related processes, and dysregulation of mitochondrial homeostasis. Our analyses highlight several specific promising pathways and genes for functional prioritization and provide a cellular context in which such work should be done.
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Affiliation(s)
- S Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - S Saez-Atienzar
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J J Kim
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M B Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - F Faghri
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M Diez-Fairen
- Fundació Docència i Recerca Mútua Terrassa and Movement Disorders Unit, Department of Neurology, University Hospital Mútua Terrassa, Terrassa, 08221, Barcelona, Spain
| | - H Iwaki
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - H Leonard
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - M Ryten
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - D Hernandez
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J R Gibbs
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J Ding
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Z Gan-Or
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - A Noyce
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London and Department of Neurology, Royal London Hospital, London, UK
| | - L Pihlstrom
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - A Torkamani
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - A R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MA, USA
| | - C L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MA, USA
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MA, USA
| | - S W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, 20892, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, 21287, USA
| | - B J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, 21287, USA
| | - D Ehrlich
- Parkinson's Disease Clinic, Office of the Clinical Director, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - C R Scherzer
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 0115, USA
| | - M Bookman
- Verily Life Sciences, South San Francisco, CA, USA
| | - M Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MA, USA
| | - C Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M A Nalls
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Data Tecnica International, Glen Echo, MD, 20812, USA
| | - A B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.
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15
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Soltis AR, Bateman NW, Conrads TP, Dalgard CL, Hu H, Franks TJ, Liu J, Meerzaman D, Petricoin EF, Chen Q, Yan C, Zhang X, Turner CE, Shriver CD, Moskaluk CA, Browning RF, Wilkerson MD. Abstract 5893: Comprehensive proteogenomic analysis and classification of lung adenocarcinoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5893] [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
Lung adenocarcinoma is a highly lethal tumor that displays extensive molecular heterogeneity of which deep characterization may drive therapeutic development and improve clinical outcomes. Through the Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) research network, we utilized five molecular profiling technologies (DNA whole genome sequencing, RNA sequencing, total and phospho-proteomics by mass spectrometry, and reverse phase protein arrays [RPPA]) to characterize a longitudinally-annotated cohort of 87 lung adenocarcinomas. Through whole genome sequencing, we identified molecular signatures from patterns of somatic SNVs, indels, and large structural alterations that stratified tumors into three groups associated with patient smoke exposures. We also identified TP53, EGFR, KRAS, and STK11 as recurrently mutated genes, which together represent 80% of the cohort, in addition to genes mutated in smaller cohort subsets (e.g. RBM10), fusion genes, and pathogenic germline variants. To characterize tumor proteomes, we quantified >7,000 proteins and >10,000 phosphopeptides by mass spectrometry and >300 species by RPPA. Matched RNAs and proteins were typically positively correlated across samples (median ρ = 0.49). Through quantitative trait loci analyses, we identified genes whose RNA and protein expression levels were significantly modified by somatic mutations. We then classified tumors into RNA expression subtypes and found coordinated proteogenomic alterations and distinct clinical associations: terminal respiratory unit subtype – EGFR mutations and RNA/protein overexpression, acinar histology, non-smokers; proximal-proliferative subtype – STK11 mutations and RNA/protein underexpression, high smoking signature; proximal-inflammatory subtype – high tumor mutational burden. We also identified phospho-peptide signatures associated with these subtypes, including downregulation of CDK1/2 targets in terminal respiratory unit tumors. Protein co-expression network analysis discovered biologically-diverse pathway activities of the RNA expression subtypes. To interrogate somatic mutations in the context of molecular pathways, we projected DNA alterations onto known interaction networks and identified four subtypes with markedly distinct proteomic and microenvironment characteristics. Finally, several molecular characteristics were found to significantly predict patient outcomes, including RNA expression subtype classification against metastasis-free survival. Thus, our integrative, proteogenomic characterization of lung adenocarcinoma uncovered novel tumor biology and identified potential molecular markers for predicting patient outcomes. The views expressed in this abstract are solely of the authors and do not reflect the official policy of the Departments of Army/Navy/Air Force, Department of Defense, USUHS, HJF, or U.S. Government.
Citation Format: Anthony R. Soltis, Nicholas W. Bateman, Thomas P. Conrads, Clifton L. Dalgard, Hai Hu, Teri J. Franks, Jianfang Liu, Daoud Meerzaman, Emanuel F. Petricoin, Qingrong Chen, Chunhua Yan, Xijun Zhang, Clesson E. Turner, The APOLLO Research Network, Craig D. Shriver, Christopher A. Moskaluk, Robert F. Browning, Matthew D. Wilkerson. Comprehensive proteogenomic analysis and classification of lung adenocarcinoma [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 5893.
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Affiliation(s)
- Anthony R. Soltis
- 1The American Genome Center, Uniformed Services University; Henry Jackson Foundation, Bethesda, MD
| | - Nicholas W. Bateman
- 2Women's Service Line at Inova Fairfax Medical Campus; Gynecologic Cancer Center of Excellence at Uniformed Services University; Henry Jackson Foundation, Falls Church, VA
| | - Thomas P. Conrads
- 3Women's Service Line at Inova Fairfax Medical Campus; Gynecologic Cancer Center of Excellence at Uniformed Services University, Falls Church, VA
| | - Clifton L. Dalgard
- 4The American Genome Center, Uniformed Services University, Bethesda, MD
| | - Hai Hu
- 5Chan Soon-Siong Institute of Molecular Medicine at Windber, Windber, PA
| | - Teri J. Franks
- 6Joint Pathology Center, Department of Defense, Silver Spring, MD
| | - Jianfang Liu
- 5Chan Soon-Siong Institute of Molecular Medicine at Windber, Windber, PA
| | - Daoud Meerzaman
- 7Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Emanuel F. Petricoin
- 8Center for Applied Proteomics and Molecular Medicine at George Mason University, Manassas, VA
| | - Qingrong Chen
- 7Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Chunhua Yan
- 7Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Xijun Zhang
- 1The American Genome Center, Uniformed Services University; Henry Jackson Foundation, Bethesda, MD
| | - Clesson E. Turner
- 9John P. Murtha Cancer Center Research Program at Uniformed Services University, Bethesda, MD
| | - Craig D. Shriver
- 9John P. Murtha Cancer Center Research Program at Uniformed Services University, Bethesda, MD
| | | | - Robert F. Browning
- 9John P. Murtha Cancer Center Research Program at Uniformed Services University, Bethesda, MD
| | - Matthew D. Wilkerson
- 1The American Genome Center, Uniformed Services University; Henry Jackson Foundation, Bethesda, MD
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16
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Soltis AR, Dalgard CL, Pollard HB, Wilkerson MD. MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes. BMC Bioinformatics 2020; 21:338. [PMID: 32736515 PMCID: PMC7393734 DOI: 10.1186/s12859-020-03695-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/15/2020] [Accepted: 07/21/2020] [Indexed: 01/23/2023] Open
Abstract
Background Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functions can be disrupted by mutation. Whole genome sequencing (WGS), on the other hand, allows for identification of non-coding somatic variation and expanded estimation of background mutation rates, yet fewer computational tools exist for specific interrogation of this space. Results We present MutEnricher, a flexible toolset for investigating somatic mutation enrichment in both coding and non-coding genomic regions from WGS data. MutEnricher contains two distinct modules for these purposes that provide customizable options for calculating sample- and feature-specific background mutation rates. Additionally, both MutEnricher modules calculate feature-level and local, or “hotspot,” somatic mutation enrichment statistics. Conclusions MutEnricher is a flexible software package for investigating somatic mutation enrichment that is implemented in Python, is freely available, can be efficiently parallelized, and is highly configurable to researcher's specific needs. MutEnricher is available online at https://github.com/asoltis/MutEnricher.
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Affiliation(s)
- Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Harvey B Pollard
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. .,Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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17
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Karim AF, Soltis AR, Sukumar G, Königs C, Ewing NP, Dalgard CL, Wilkerson MD, Pratt KP. Hemophilia A Inhibitor Subjects Show Unique PBMC Gene Expression Profiles That Include Up-Regulated Innate Immune Modulators. Front Immunol 2020; 11:1219. [PMID: 32595650 PMCID: PMC7303277 DOI: 10.3389/fimmu.2020.01219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022] Open
Abstract
Formation of pathological anti-FVIII antibodies, or "inhibitors," is the most serious complication of therapeutic FVIII infusions, affecting up to 1/3 of severe Hemophilia A (HA) patients. Inhibitor formation is a classical T-cell dependent adaptive immune response. As such, it requires help from the innate immune system. However, the roles of innate immune cells and mechanisms of inhibitor development vs. immune tolerance, achieved with or without Immune Tolerance Induction (ITI) therapy, are not well-understood. To address these questions, temporal transcriptomics profiling of FVIII-stimulated peripheral blood mononuclear cells (PBMCs) was carried out for HA subjects with and without a current or historic inhibitor using RNA-Seq. PBMCs were isolated from 40 subjects in the following groups: HA with an inhibitor that resolved either following ITI or spontaneously; HA with a current inhibitor; HA with no inhibitor history and non-HA controls. PBMCs were stimulated with 5 nM FVIII and RNA was isolated 4, 16, 24, and 48 h following stimulation. Time-series differential expression analysis was performed and distinct transcriptional signatures were identified for each group, providing clues as to cellular mechanisms leading to or accompanying their disparate anti-FVIII antibody responses. Subjects with a current inhibitor showed differential expression of 56 genes and a clustering analysis identified three major temporal profiles. Interestingly, gene ontology enrichments featured innate immune modulators, including NLRP3, TLR8, IL32, CLEC10A, and COLEC12. NLRP3 and TLR8 are associated with enhanced secretion of the pro-inflammatory cytokines IL-1β and TNFα, while IL32, which has several isoforms, has been associated with both inflammatory and regulatory immune processes. RNA-Seq results were validated by RT-qPCR, ELISAs, multiplex cytokine analysis, and flow cytometry. The inflammatory status of HA patients suffering from an ongoing inhibitor includes up-regulated innate immune modulators, which may act as ongoing danger signals that influence the responses to, and eventual outcomes of, ITI therapy.
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Affiliation(s)
- Ahmad Faisal Karim
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Anthony R Soltis
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Collaborative Health Initiative Research Program, Henry Jackson Foundation for the Advancement of Military Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Gauthaman Sukumar
- Collaborative Health Initiative Research Program, Henry Jackson Foundation for the Advancement of Military Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | | | - Nadia P Ewing
- City of Hope National Medical Center, Duarte, CA, United States
| | - Clifton L Dalgard
- Collaborative Health Initiative Research Program, Henry Jackson Foundation for the Advancement of Military Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Matthew D Wilkerson
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Collaborative Health Initiative Research Program, Henry Jackson Foundation for the Advancement of Military Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kathleen P Pratt
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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18
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Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK. Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer. Cell Rep 2020; 31:107502. [PMID: 32294438 PMCID: PMC7234854 DOI: 10.1016/j.celrep.2020.03.066] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [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: 08/28/2019] [Revised: 01/02/2020] [Accepted: 03/19/2020] [Indexed: 12/30/2022] Open
Abstract
The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC), which is the most lethal gynecologic malignancy, is not well understood. Here, we perform comprehensive multi-platform omics analyses, including integrated analysis, and immune monitoring on primary and metastatic sites from highly clinically annotated HGSC samples based on a laparoscopic triage algorithm from patients who underwent complete gross resection (R0) or received neoadjuvant chemotherapy (NACT) with excellent or poor response. We identify significant distinct molecular abnormalities and cellular changes and immune cell repertoire alterations between the groups, including a higher rate of NF1 copy number loss, and reduced chromothripsis-like patterns, higher levels of strong-binding neoantigens, and a higher number of infiltrated T cells in the R0 versus the NACT groups.
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Affiliation(s)
- Sanghoon Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christine Rojas
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Nicholas W Bateman
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Olivia D Lara
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph Celestino
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret B Morgan
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tri V Nguyen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelly A Conrads
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kelly M Rangel
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert L Dood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard A Hajek
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gloria L Fawcett
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Randy A Chu
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katlin Wilson
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jeremy L Loffredo
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Coralie Viollet
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xizeng Mao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming Zhou
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Brian L Hood
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Nirad Banskota
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jerez Te
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | | | | | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared K Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith A Baggerly
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole D Fleming
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen H Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shannon N Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert L Coleman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - George L Maxwell
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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19
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Yang Q, Soltis AR, Sukumar G, Zhang X, Caohuy H, Freedy J, Dalgard CL, Wilkerson MD, Pollard HB, Pollard BS. Gene therapy-emulating small molecule treatments in cystic fibrosis airway epithelial cells and patients. Respir Res 2019; 20:290. [PMID: 31864360 PMCID: PMC6925517 DOI: 10.1186/s12931-019-1214-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 03/11/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
Background Several small molecule corrector and potentiator drugs have recently been licensed for Cystic Fibrosis (CF) therapy. However, other aspects of the disease, especially inflammation, are less effectively treated by these drugs. We hypothesized that small molecule drugs could function either alone or as an adjuvant to licensed therapies to treat these aspects of the disease, perhaps emulating the effects of gene therapy in CF cells. The cardiac glycoside digitoxin, which has been shown to inhibit TNFα/NFκB signaling in CF lung epithelial cells, may serve as such a therapy. Methods IB3–1 CF lung epithelial cells were treated with different Vertex (VX) drugs, digitoxin, and various drug mixtures, and ELISA assays were used to assess suppression of baseline and TNFα-activated secretion of cytokines and chemokines. Transcriptional responses to these drugs were assessed by RNA-seq and compared with gene expression in AAV-[wildtype]CFTR-treated IB3–1 (S9) cells. We also compared in vitro gene expression signatures with in vivo data from biopsied nasal epithelial cells from digitoxin-treated CF patients. Results CF cells exposed to digitoxin exhibited significant suppression of both TNFα/NFκB signaling and downstream secretion of IL-8, IL-6 and GM-CSF, with or without co-treatment with VX drugs. No evidence of drug-drug interference was observed. RNA-seq analysis showed that gene therapy-treated CF lung cells induced changes in 3134 genes. Among these, 32.6% were altered by digitoxin treatment in the same direction. Shared functional gene ontology themes for genes suppressed by both digitoxin and gene therapy included inflammation (84 gene signature), and cell-cell interactions and fibrosis (49 gene signature), while genes elevated by both were enriched for epithelial differentiation (82 gene signature). A new analysis of mRNA data from digitoxin-treated CF patients showed consistent trends in expression for genes in these signatures. Conclusions Adjuvant gene therapy-emulating activities of digitoxin may contribute to enhancing the efficacy of currently licensed correctors and potentiators in CF patients.
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Affiliation(s)
- Q Yang
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - A R Soltis
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - G Sukumar
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - X Zhang
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - H Caohuy
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - J Freedy
- Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - C L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA.,Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - M D Wilkerson
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA.,Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA
| | - H B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine- America's Medical School, Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA. .,Collaborative Health Initiative Research Program (CHIRP), The American Genome Center (TAGC), Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD, 20814, USA.
| | - B S Pollard
- Silver Pharmaceuticals, Rockville, MD, 20854, USA.
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20
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Voss K, Lake C, Luthers CR, Lott NM, Dorjbal B, Arjunaraja S, Bauman BM, Soltis AR, Sukumar G, Dalgard CL, Snow AL. FOXP3 protects conventional human T cells from premature restimulation-induced cell death. Cell Mol Immunol 2019; 18:194-205. [PMID: 31659245 DOI: 10.1038/s41423-019-0316-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/02/2019] [Indexed: 02/01/2023] Open
Abstract
The adaptive immune response relies on specific apoptotic programs to maintain homeostasis. Conventional effector T cell (Tcon) expansion is constrained by both forkhead box P3 (FOXP3)+-regulatory T cells (Tregs) and restimulation-induced cell death (RICD), a propriocidal apoptosis pathway triggered by repeated stimulation through the T-cell receptor (TCR). Constitutive FOXP3 expression protects Tregs from RICD by suppressing SLAM-associated protein (SAP), a key adaptor protein that amplifies TCR signaling strength. The role of transient FOXP3 induction in activated human CD4 and CD8 Tcons remains unresolved, but its expression is inversely correlated with acquired RICD sensitivity. Here, we describe a novel role for FOXP3 in protecting human Tcons from premature RICD during expansion. Unlike FOXP3-mediated protection from RICD in Tregs, FOXP3 protects Tcons through a distinct mechanism requiring de novo transcription that does not require SAP suppression. Transcriptome profiling and functional analyses of expanding Tcons revealed that FOXP3 enhances expression of the SLAM family receptor CD48, which in turn sustains basal autophagy and suppresses pro-apoptotic p53 signaling. Both CD48 and FOXP3 expression reduced p53 accumulation upon TCR restimulation. Furthermore, silencing FOXP3 expression or blocking CD48 decreased the mitochondrial membrane potential in expanding Tcons with a concomitant reduction in basal autophagy. Our findings suggest that FOXP3 governs a distinct transcriptional program in early-stage effector Tcons that maintains RICD resistance via CD48-dependent protective autophagy and p53 suppression.
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Affiliation(s)
- Kelsey Voss
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20817, USA
| | - Camille Lake
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20817, USA
| | - Christopher R Luthers
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20817, USA
| | - Nathaniel M Lott
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Batsukh Dorjbal
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20817, USA
| | - Swadhinya Arjunaraja
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20817, USA
| | - Bradly M Bauman
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20817, USA
| | - Anthony R Soltis
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gauthaman Sukumar
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center (TAGC), Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20817, USA.
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21
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Conrads T, Tarney C, Bateman N, Soltis AR, Hood BL, Dalgard CL, Wilkerson M, Darcy KM, Casablanca Y, Al-Hendy A, Segars J, Maxwell GL. Multi-omic analysis of uterine leiomyomas from hereditary leiomyomatosis and renal cell cancer patients. Fertil Steril 2019. [DOI: 10.1016/j.fertnstert.2019.07.999] [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: 11/30/2022]
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22
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Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB. Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes. Cancer Res 2019; 79:1952-1966. [PMID: 30755444 PMCID: PMC6467770 DOI: 10.1158/0008-5472.can-18-1604] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [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: 05/25/2018] [Revised: 09/19/2018] [Accepted: 02/06/2019] [Indexed: 01/07/2023]
Abstract
Acidosis is a fundamental feature of the tumor microenvironment, which directly regulates tumor cell invasion by affecting immune cell function, clonal cell evolution, and drug resistance. Despite the important association of tumor microenvironment acidosis with tumor cell invasion, relatively little is known regarding which areas within a tumor are acidic and how acidosis influences gene expression to promote invasion. Here, we injected a labeled pH-responsive peptide to mark acidic regions within tumors. Surprisingly, acidic regions were not restricted to hypoxic areas and overlapped with highly proliferative, invasive regions at the tumor-stroma interface, which were marked by increased expression of matrix metalloproteinases and degradation of the basement membrane. RNA-seq analysis of cells exposed to low pH conditions revealed a general rewiring of the transcriptome that involved RNA splicing and enriched for targets of RNA binding proteins with specificity for AU-rich motifs. Alternative splicing of Mena and CD44, which play important isoform-specific roles in metastasis and drug resistance, respectively, was sensitive to histone acetylation status. Strikingly, this program of alternative splicing was reversed in vitro and in vivo through neutralization experiments that mitigated acidic conditions. These findings highlight a previously underappreciated role for localized acidification of tumor microenvironment in the expression of an alternative splicing-dependent tumor invasion program. SIGNIFICANCE: This study expands our understanding of acidosis within the tumor microenvironment and indicates that acidosis induces potentially therapeutically actionable changes to alternative splicing.
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Affiliation(s)
- Nazanin Rohani
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts.
| | - Liangliang Hao
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Maria S Alexis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
| | - Konstantin Krismer
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts
| | - Mira N Moufarrej
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | - Anthony R Soltis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
| | | | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Department of Biological Engineering, MIT, Cambridge, Massachusetts
- Center for Precision Cancer Medicine, MIT, Cambridge, Massachusetts
- Department of Biology, MIT, Cambridge, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | | | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Cambridge, Massachusetts
| | - Frank B Gertler
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts.
- Department of Biology, MIT, Cambridge, Massachusetts
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Oyola MG, Shupe EA, Soltis AR, Sukumar G, Paez-Pereda M, Larco DO, Wilkerson MD, Rothwell S, Dalgard CL, Wu TJ. Sleep Deprivation Alters the Pituitary Stress Transcriptome in Male and Female Mice. Front Endocrinol (Lausanne) 2019; 10:676. [PMID: 31649619 PMCID: PMC6794367 DOI: 10.3389/fendo.2019.00676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/18/2019] [Indexed: 01/02/2023] Open
Abstract
Poor sleep hygiene is a growing problem, with detrimental effects on many biological systems. The pituitary gland plays a crucial role in the regulation of sleep and the stress response, and its dysfunction leads to sleep-related disorders. However, the interaction between these critical functions remains unclear. Thus, we performed a comparative, whole-transcriptome, analysis to identify stress-induced genes and relevant pathways that may be affected by sleep deprivation. One day following 12 h of Paradoxical Sleep Deprivation (PSD), mice were restrained for 20 min. Gene expression changes in the pituitary were assessed via RNA-Seq and Gene Ontology in PSD and/or restrained groups compared to controls. We show that restraint triggers transcriptional responses involved in hormone secretion, the glucocorticoid response, and apoptosis in both sexes, with 285 differentially expressed genes in females and 93 in males. When PSD preceded restraint stress, the numbers of differentially expressed genes increased to 613 in females and 580 in males. The pituitary transcriptome of restraint+PSD animals was enriched for microglia and macrophage proliferation, cellular response to corticosteroids, and apoptosis, among others. Finally, we identify sex-specific differences in restraint-induced genes following PSD. These findings provide genetic targets to consider when studying sleep and the response to stress.
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Affiliation(s)
- Mario G. Oyola
- Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Center for Neuroscience and Regenerative Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Elizabeth A. Shupe
- Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Anthony R. Soltis
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Marcelo Paez-Pereda
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Darwin O. Larco
- Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Matthew D. Wilkerson
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Stephen Rothwell
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Clifton L. Dalgard
- Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - T. John Wu
- Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Center for Neuroscience and Regenerative Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- *Correspondence: T. John Wu
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Soltis AR, Viollet C, Pollard HB, Moskaluk CA, Browning RF, Dalgard CL, Shriver CD, Wilkerson MD. Abstract 2281: Flexible discovery of recurrent coding and non-coding mutations in tumor whole genomes. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2281] [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
Analysis of somatic protein-coding mutations, particularly via tumor exome sequencing, has driven discovery of novel cancer genes in recent years. However, ~97% of the human genome is non-coding and not addressable by exome-targeting methods. Tumor whole genome sequencing, by contrast, allows for genome-wide discovery of somatic events and may identify novel non-coding driver mutations. In conjunction, flexible tools employing principled statistical methods are needed for discovery of recurrent somatic driver mutations from tumor whole genomes.
Here, we developed a computational toolset that addresses these needs and describe its application to a novel cohort of lung adenocarcinoma tumors generated by the APOLLO (Applied Proteogenomics OrganizationaL Learning and Outcomes) consortium. Our toolset flexibly computes feature-wise and hotspot somatic mutation enrichment statistics in both protein-coding and non-coding (e.g. promoters, enhancers) genomic regions. Additionally, we incorporated an affinity propagation-based clustering procedure that groups test regions by user-specified genomic covariates that can influence local mutation properties.
We applied our toolset to several TCGA datasets of tumor exome sequencing. We found strong agreement between our results and those of other tools: among the top 15 genes called at FDR < 0.01 by MutSigCV, we observed a median overlap of 75.7% with genes ranked in the top 15 by our methods. We next applied our toolset to tumor whole genome sequencing data from our APOLLO lung adenocarcinoma cohort. During analysis, we simultaneously controlled for several genomic covariates, including GC/CpG content, replication timing, and proximal mRNA expression. Gene-centric analysis identified several significantly mutated genes, including KRAS, STK11, and TP53 (FDR < 0.005). We examined matched mRNA-seq data from this cohort and found significant over-expression of KRAS mRNA in samples possessing a non-silent coding mutation in this gene (p < 0.02). We additionally assessed somatic mutation enrichment in promoters, 3' UTRs, non-coding genes, and lung-specific enhancers. From these results, we found significant enrichment of somatic mutations in the body of the long non-coding RNA NEAT1. Among the tumors with somatic NEAT1 mutations, a single sample was hypermutated at this locus and corresponded with the lowest observed RNA expression for this lncRNA in our cohort (TPM of 12.2 vs. overall mean TPM of 84.2).
In conclusion, we developed a flexible toolset for interrogating both coding and non-coding landscapes from tumor whole genomes. We applied our methods to a novel cohort of lung adenocarcinoma tumors and identified recurrently mutated genes and non-coding regions, including the NEAT1 lncRNA.
Citation Format: Anthony R. Soltis, Coralie Viollet, Harvey B. Pollard, Christopher A. Moskaluk, Robert F. Browning, Clifton L. Dalgard, Craig D. Shriver, Matthew D. Wilkerson. Flexible discovery of recurrent coding and non-coding mutations in tumor whole genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2281.
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Affiliation(s)
- Anthony R. Soltis
- 1The American Genome Center at the Uniformed Services University, Bethesda, MD
| | - Coralie Viollet
- 1The American Genome Center at the Uniformed Services University, Bethesda, MD
| | - Harvey B. Pollard
- 1The American Genome Center at the Uniformed Services University, Bethesda, MD
| | | | | | - Clifton L. Dalgard
- 4The American Genome Center at the Uniformed Services University and John P. Murtha Cancer Center, Bethesda, MD
| | - Craig D. Shriver
- 5John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD
| | - Matthew D. Wilkerson
- 4The American Genome Center at the Uniformed Services University and John P. Murtha Cancer Center, Bethesda, MD
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Tuncbag N, Gosline SJC, Kedaigle A, Soltis AR, Gitter A, Fraenkel E. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PLoS Comput Biol 2016; 12:e1004879. [PMID: 27096930 PMCID: PMC4838263 DOI: 10.1371/journal.pcbi.1004879] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [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: 07/17/2015] [Accepted: 03/23/2016] [Indexed: 02/07/2023] Open
Abstract
High-throughput, ‘omic’ methods provide sensitive measures of biological responses to perturbations. However, inherent biases in high-throughput assays make it difficult to interpret experiments in which more than one type of data is collected. In this work, we introduce Omics Integrator, a software package that takes a variety of ‘omic’ data as input and identifies putative underlying molecular pathways. The approach applies advanced network optimization algorithms to a network of thousands of molecular interactions to find high-confidence, interpretable subnetworks that best explain the data. These subnetworks connect changes observed in gene expression, protein abundance or other global assays to proteins that may not have been measured in the screens due to inherent bias or noise in measurement. This approach reveals unannotated molecular pathways that would not be detectable by searching pathway databases. Omics Integrator also provides an elegant framework to incorporate not only positive data, but also negative evidence. Incorporating negative evidence allows Omics Integrator to avoid unexpressed genes and avoid being biased toward highly-studied hub proteins, except when they are strongly implicated by the data. The software is comprised of two individual tools, Garnet and Forest, that can be run together or independently to allow a user to perform advanced integration of multiple types of high-throughput data as well as create condition-specific subnetworks of protein interactions that best connect the observed changes in various datasets. It is available at http://fraenkel.mit.edu/omicsintegrator and on GitHub at https://github.com/fraenkel-lab/OmicsIntegrator.
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Affiliation(s)
- Nurcan Tuncbag
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sara J. C. Gosline
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Amanda Kedaigle
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anthony R. Soltis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anthony Gitter
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Soltis AR, Saucerman JJ. Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty. ACTA ACUST UNITED AC 2011; 27:2888-94. [PMID: 21880701 DOI: 10.1093/bioinformatics/btr496] [Citation(s) in RCA: 13] [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: 11/13/2022]
Abstract
MOTIVATION Biological networks are robust to a wide variety of internal and external perturbations, yet fragile or sensitive to a small minority of perturbations. Due to this rare sensitivity of networks to certain perturbations, it is unclear how precisely biochemical parameters must be experimentally measured in order to accurately predict network function. RESULTS Here, we examined a model of cardiac β-adrenergic signaling and found that its robustness portrait, a global measure of steady-state network function, was well conserved even when all parameters were rounded to their nearest 1-2 orders of magnitude. In contrast, β-adrenergic network kinetics were more sensitive to parameter precision. This analysis was then extended to 10 additional networks, including Escherichia coli chemotaxis, stem cell differentiation and cytokine signaling, of which nine exhibited conserved robustness portraits despite the order-of-magnitude approximation of their biochemical parameters. Thus, both fragile and robust aspects of diverse biological networks are largely shaped by network topology and can be predicted despite order-of-magnitude uncertainty in biochemical parameters. These findings suggest an iterative strategy where order-of-magnitude models are used to prioritize experiments toward the fragile network elements that require precise measurements, efficiently driving model revision. CONTACT jsaucerman@virginia.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anthony R Soltis
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
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Soltis AR, Saucerman JJ. Synergy between CaMKII substrates and β-adrenergic signaling in regulation of cardiac myocyte Ca(2+) handling. Biophys J 2011; 99:2038-47. [PMID: 20923637 DOI: 10.1016/j.bpj.2010.08.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 07/23/2010] [Accepted: 08/04/2010] [Indexed: 01/10/2023] Open
Abstract
Cardiac excitation-contraction coupling is a highly coordinated process that is controlled by protein kinase signaling pathways, including Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) and protein kinase A (PKA). Increased CaMKII expression and activity (as occurs during heart failure) destabilizes EC coupling and may lead to sudden cardiac death. To better understand mechanisms of cardiac CaMKII function, we integrated dynamic CaMKII-dependent regulation of key Ca(2+) handling targets with previously validated models of cardiac EC coupling, Ca(2+)/calmodulin-dependent activation of CaMKII, and β-adrenergic activation of PKA. Model predictions are validated against CaMKII-overexpression data from rabbit ventricular myocytes. The model demonstrates how overall changes to Ca(2+) handling during CaMKII overexpression are explained by interactions between individual CaMKII substrates. CaMKII and PKA activities during β-adrenergic stimulation may synergistically facilitate inotropic responses and contribute to a CaMKII-Ca(2+)-CaMKII feedback loop. CaMKII regulated early frequency-dependent acceleration of relaxation and EC coupling gain (which was highly sarcoplasmic reticulum Ca(2+) load-dependent). Additionally, the model identifies CaMKII-dependent ryanodine receptor hyperphosphorylation as a proarrhythmogenic trigger. In summary, we developed a detailed computational model of CaMKII and PKA signaling in cardiac myocytes that provides unique insights into their regulation of normal and pathological Ca(2+) handling.
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Affiliation(s)
- Anthony R Soltis
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
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Kraeutler MJ, Soltis AR, Saucerman JJ. Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model. BMC Syst Biol 2010; 4:157. [PMID: 21087478 PMCID: PMC2993667 DOI: 10.1186/1752-0509-4-157] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 11/18/2010] [Indexed: 12/11/2022]
Abstract
Background New approaches are needed for large-scale predictive modeling of cellular signaling networks. While mass action and enzyme kinetic approaches require extensive biochemical data, current logic-based approaches are used primarily for qualitative predictions and have lacked direct quantitative comparison with biochemical models. Results We developed a logic-based differential equation modeling approach for cell signaling networks based on normalized Hill activation/inhibition functions controlled by logical AND and OR operators to characterize signaling crosstalk. Using this approach, we modeled the cardiac β1-adrenergic signaling network, including 36 reactions and 25 species. Direct comparison of this model to an extensively characterized and validated biochemical model of the same network revealed that the new model gave reasonably accurate predictions of key network properties, even with default parameters. Normalized Hill functions improved quantitative predictions of global functional relationships compared with prior logic-based approaches. Comprehensive sensitivity analysis revealed the significant role of PKA negative feedback on upstream signaling and the importance of phosphodiesterases as key negative regulators of the network. The model was then extended to incorporate recently identified protein interaction data involving integrin-mediated mechanotransduction. Conclusions The normalized-Hill differential equation modeling approach allows quantitative prediction of network functional relationships and dynamics, even in systems with limited biochemical data.
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Affiliation(s)
- Matthew J Kraeutler
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
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