1
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Graves AJ, Danoff JS, Kim M, Brindley SR, Skyberg AM, Giamberardino SN, Lynch ME, Straka BC, Lillard TS, Gregory SG, Connelly JJ, Morris JP. Accelerated epigenetic age is associated with whole-brain functional connectivity and impaired cognitive performance in older adults. Sci Rep 2024; 14:9646. [PMID: 38671048 PMCID: PMC11053089 DOI: 10.1038/s41598-024-60311-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024] Open
Abstract
While chronological age is a strong predictor for health-related risk factors, it is an incomplete metric that fails to fully characterize the unique aging process of individuals with different genetic makeup, neurodevelopment, and environmental experiences. Recent advances in epigenomic array technologies have made it possible to generate DNA methylation-based biomarkers of biological aging, which may be useful in predicting a myriad of cognitive abilities and functional brain network organization across older individuals. It is currently unclear which cognitive domains are negatively correlated with epigenetic age above and beyond chronological age, and it is unknown if functional brain organization is an important mechanism for explaining these associations. In this study, individuals with accelerated epigenetic age (i.e. AgeAccelGrim) performed worse on tasks that spanned a wide variety of cognitive faculties including both fluid and crystallized intelligence (N = 103, average age = 68.98 years, 73 females, 30 males). Additionally, fMRI connectome-based predictive models suggested a mediating mechanism of functional connectivity on epigenetic age acceleration-cognition associations primarily in medial temporal lobe and limbic structures. This research highlights the important role of epigenetic aging processes on the development and maintenance of healthy cognitive capacities and function of the aging brain.
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Affiliation(s)
| | | | - Minah Kim
- University of Virginia, Charlottesville, USA
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2
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Liu M, Ji Z, Jain V, Smith VL, Hocke E, Patel AP, McLendon RE, Ashley DM, Gregory SG, López GY. Spatial transcriptomics reveals segregation of tumor cell states in glioblastoma and marked immunosuppression within the perinecrotic niche. Acta Neuropathol Commun 2024; 12:64. [PMID: 38650010 PMCID: PMC11036705 DOI: 10.1186/s40478-024-01769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/30/2024] [Indexed: 04/25/2024] Open
Abstract
Glioblastoma (GBM) remains an untreatable malignant tumor with poor patient outcomes, characterized by palisading necrosis and microvascular proliferation. While single-cell technology made it possible to characterize different lineage of glioma cells into neural progenitor-like (NPC-like), oligodendrocyte-progenitor-like (OPC-like), astrocyte-like (AC-like) and mesenchymal like (MES-like) states, it does not capture the spatial localization of these tumor cell states. Spatial transcriptomics empowers the study of the spatial organization of different cell types and tumor cell states and allows for the selection of regions of interest to investigate region-specific and cell-type-specific pathways. Here, we obtained paired 10x Chromium single-nuclei RNA-sequencing (snRNA-seq) and 10x Visium spatial transcriptomics data from three GBM patients to interrogate the GBM microenvironment. Integration of the snRNA-seq and spatial transcriptomics data reveals patterns of segregation of tumor cell states. For instance, OPC-like tumor and NPC-like tumor significantly segregate in two of the three samples. Our differentially expressed gene and pathway analyses uncovered significant pathways in functionally relevant niches. Specifically, perinecrotic regions were more immunosuppressive than the endogenous GBM microenvironment, and perivascular regions were more pro-inflammatory. Our gradient analysis suggests that OPC-like tumor cells tend to reside in areas closer to the tumor vasculature compared to tumor necrosis, which may reflect increased oxygen requirements for OPC-like cells. In summary, we characterized the localization of cell types and tumor cell states, the gene expression patterns, and pathways in different niches within the GBM microenvironment. Our results provide further evidence of the segregation of tumor cell states and highlight the immunosuppressive nature of the necrotic and perinecrotic niches in GBM.
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Affiliation(s)
- Mengyi Liu
- Computational Biology and Bioinformatics Program, Duke University School of Medicine, Durham, NC, 27710, USA
- The Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, 27705, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, 27705, USA
| | - Vanessa L Smith
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Emily Hocke
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, 27705, USA
| | - Anoop P Patel
- The Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Roger E McLendon
- The Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Simon G Gregory
- The Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, 27705, USA.
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Giselle Y López
- The Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
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3
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Epstein AA, Janos SN, Menozzi L, Pegram K, Jain V, Bisset LC, Davis JT, Morrison S, Shailaja A, Guo Y, Chao AS, Abdi K, Rikard B, Yao J, Gregory SG, Fisher K, Pittman R, Erkanli A, Gustafson KE, Carrico CWT, Malcolm WF, Inder TE, Cotten CM, Burt TD, Shinohara ML, Maxfield CM, Benner EJ. Subventricular zone stem cell niche injury is associated with intestinal perforation in preterm infants and predicts future motor impairment. Cell Stem Cell 2024; 31:467-483.e6. [PMID: 38537631 DOI: 10.1016/j.stem.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 02/11/2024] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Brain injury is highly associated with preterm birth. Complications of prematurity, including spontaneous or necrotizing enterocolitis (NEC)-associated intestinal perforations, are linked to lifelong neurologic impairment, yet the mechanisms are poorly understood. Early diagnosis of preterm brain injuries remains a significant challenge. Here, we identified subventricular zone echogenicity (SVE) on cranial ultrasound in preterm infants following intestinal perforations. The development of SVE was significantly associated with motor impairment at 2 years. SVE was replicated in a neonatal mouse model of intestinal perforation. Examination of the murine echogenic subventricular zone (SVZ) revealed NLRP3-inflammasome assembly in multiciliated FoxJ1+ ependymal cells and a loss of the ependymal border in this postnatal stem cell niche. These data suggest a mechanism of preterm brain injury localized to the SVZ that has not been adequately considered. Ultrasound detection of SVE may serve as an early biomarker for neurodevelopmental impairment after inflammatory disease in preterm infants.
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Affiliation(s)
- Adrian A Epstein
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Sara N Janos
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Luca Menozzi
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Kelly Pegram
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Logan C Bisset
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Joseph T Davis
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Samantha Morrison
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Aswathy Shailaja
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Yingqiu Guo
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Agnes S Chao
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Khadar Abdi
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Blaire Rikard
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA; Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Kimberley Fisher
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Rick Pittman
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Al Erkanli
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Kathryn E Gustafson
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | | | - William F Malcolm
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Terrie E Inder
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - C Michael Cotten
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA
| | - Trevor D Burt
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA; Children's Health and Discovery Initiative, Duke University School of Medicine, Durham, NC, USA
| | - Mari L Shinohara
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Charles M Maxfield
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA.
| | - Eric J Benner
- Department of Pediatrics, Division of Neonatology, Duke University School of Medicine, Durham, NC, USA; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA.
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4
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Duchatel RJ, Jackson ER, Parackal SG, Kiltschewskij D, Findlay IJ, Mannan A, Staudt DE, Thomas BC, Germon ZP, Laternser S, Kearney PS, Jamaluddin MFB, Douglas AM, Beitaki T, McEwen HP, Persson ML, Hocke EA, Jain V, Aksu M, Manning EE, Murray HC, Verrills NM, Sun CX, Daniel P, Vilain RE, Skerrett-Byrne DA, Nixon B, Hua S, de Bock CE, Colino-Sanguino Y, Valdes-Mora F, Tsoli M, Ziegler DS, Cairns MJ, Raabe EH, Vitanza NA, Hulleman E, Phoenix TN, Koschmann C, Alvaro F, Dayas CV, Tinkle CL, Wheeler H, Whittle JR, Eisenstat DD, Firestein R, Mueller S, Valvi S, Hansford JR, Ashley DM, Gregory SG, Kilburn LB, Nazarian J, Cain JE, Dun MD. PI3K/mTOR is a therapeutically targetable genetic dependency in diffuse intrinsic pontine glioma. J Clin Invest 2024; 134:e170329. [PMID: 38319732 PMCID: PMC10940093 DOI: 10.1172/jci170329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Diffuse midline glioma (DMG), including tumors diagnosed in the brainstem (diffuse intrinsic pontine glioma; DIPG), are uniformly fatal brain tumors that lack effective treatment. Analysis of CRISPR/Cas9 loss-of-function gene deletion screens identified PIK3CA and MTOR as targetable molecular dependencies across patient derived models of DIPG, highlighting the therapeutic potential of the blood-brain barrier-penetrant PI3K/Akt/mTOR inhibitor, paxalisib. At the human-equivalent maximum tolerated dose, mice treated with paxalisib experienced systemic glucose feedback and increased insulin levels commensurate with patients using PI3K inhibitors. To exploit genetic dependence and overcome resistance while maintaining compliance and therapeutic benefit, we combined paxalisib with the antihyperglycemic drug metformin. Metformin restored glucose homeostasis and decreased phosphorylation of the insulin receptor in vivo, a common mechanism of PI3K-inhibitor resistance, extending survival of orthotopic models. DIPG models treated with paxalisib increased calcium-activated PKC signaling. The brain penetrant PKC inhibitor enzastaurin, in combination with paxalisib, synergistically extended the survival of multiple orthotopic patient-derived and immunocompetent syngeneic allograft models; benefits potentiated in combination with metformin and standard-of-care radiotherapy. Therapeutic adaptation was assessed using spatial transcriptomics and ATAC-Seq, identifying changes in myelination and tumor immune microenvironment crosstalk. Collectively, this study has identified what we believe to be a clinically relevant DIPG therapeutic combinational strategy.
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Affiliation(s)
- Ryan J. Duchatel
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Evangeline R. Jackson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Sarah G. Parackal
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Dylan Kiltschewskij
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Izac J. Findlay
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Abdul Mannan
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Dilana E. Staudt
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Bryce C. Thomas
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Zacary P. Germon
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Sandra Laternser
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
| | - Padraic S. Kearney
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - M. Fairuz B. Jamaluddin
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Alicia M. Douglas
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Tyrone Beitaki
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Holly P. McEwen
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Mika L. Persson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
| | - Emily A. Hocke
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael Aksu
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Elizabeth E. Manning
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Heather C. Murray
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Nicole M. Verrills
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Claire Xin Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Paul Daniel
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Ricardo E. Vilain
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - David A. Skerrett-Byrne
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Brett Nixon
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Susan Hua
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Charles E. de Bock
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Yolanda Colino-Sanguino
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Fatima Valdes-Mora
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - Maria Tsoli
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
| | - David S. Ziegler
- Children’s Cancer Institute, University of New South Wales (UNSW) Sydney, Kensington, New South Wales, Australia
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Kensington, New South Wales, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Murray J. Cairns
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Eric H. Raabe
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicholas A. Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle, Washington, USA
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Timothy N. Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, Ohio, USA
| | - Carl Koschmann
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank Alvaro
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- John Hunter Children’s Hospital, New Lambton Heights, New South Wales, Australia
| | - Christopher V. Dayas
- School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Christopher L. Tinkle
- Department of Radiation Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Helen Wheeler
- Department of Radiation Oncology Northern Sydney Cancer Centre, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- The Brain Cancer group, St Leonards, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - James R. Whittle
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David D. Eisenstat
- Children’s Cancer Centre, The Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
- Neuro-Oncology Laboratory, Murdoch Children’s Research Institute, Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Sabine Mueller
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
- Department of Neurology, Neurosurgery, and Pediatrics, University of California, San Francisco, California, USA
| | - Santosh Valvi
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children’s Hospital, Nedlands, Washington, Australia
- Brain Tumour Research Laboratory, Telethon Kids Institute, Nedlands, Washington, Australia
- Division of Paediatrics, University of Western Australia Medical School, Nedlands, Western Australia, Australia
| | - Jordan R. Hansford
- Michael Rice Centre for Hematology and Oncology, Women’s and Children’s Hospital, North Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - David M. Ashley
- The Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
- The Preston Robert Tisch Brain Tumor Center at Duke, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Lindsay B. Kilburn
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- The George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Javad Nazarian
- DIPG/DMG Research Center Zurich, Children’s Research Center, Department of Pediatrics, University Children’s Hospital Zürich, Zurich, Switzerland
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- The George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Jason E. Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- Paediatric Stream, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine, and Wellbeing, Callaghan, New South Wales, Australia
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5
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Dalton GD, Siecinski SK, Nikolova VD, Cofer GP, Hornburg K, Qi Y, Johnson GA, Jiang YH, Moy SS, Gregory SG. Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability. bioRxiv 2024:2024.01.15.575733. [PMID: 38293238 PMCID: PMC10827122 DOI: 10.1101/2024.01.15.575733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with higher incidence in males and is characterized by atypical verbal/nonverbal communication, restricted interests that can be accompanied by repetitive behavior, and disturbances in social behavior. This study investigated brain mechanisms that contribute to sociability deficits and sex differences in an ASD animal model. Methods Sociability was measured in C58/J and C57BL/6J mice using the 3-chamber social choice test. Bulk RNA-Seq and snRNA-Seq identified transcriptional changes in C58/J and C57BL/6J amygdala within which DMRseq was used to measure differentially methylated regions in amygdala. Results C58/J mice displayed divergent social strata in the 3-chamber test. Transcriptional and pathway signatures revealed immune-related biological processes differ between C58/J and C57BL/6J amygdala. Hypermethylated and hypomethylated genes were identified in C58/J versus C57BL/6J amygdala. snRNA-Seq data in C58/J amygdala identified differential transcriptional signatures within oligodendrocytes and microglia characterized by increased ASD risk gene expression and predicted impaired myelination that was dependent on sex and sociability. RNA velocity, gene regulatory network, and cell communication analysis showed diminished oligodendrocyte/microglia differentiation. Findings were verified using bulk RNA-Seq and demonstrated oxytocin's beneficial effects on myelin gene expression. Limitations Our findings are significant. However, limitations can be noted. The cellular mechanisms linking reduced oligodendrocyte differentiation and reduced myelination to an ASD phenotype in C58/J mice need further investigation. Additional snRNA-Seq and spatial studies would determine if effects in oligodendrocytes/microglia are unique to amygdala or if this occurs in other brain regions. Oxytocin's effects need further examination to understand its potential as an ASD therapeutic. Conclusions Our work demonstrates the C58/J mouse model's utility in evaluating the influence of sex and sociability on the transcriptome in concomitant brain regions involved in ASD. Our single-nucleus transcriptome analysis elucidates potential pathological roles of oligodendrocytes and microglia in ASD. This investigation provides details regarding regulatory features disrupted in these cell types, including transcriptional gene dysregulation, aberrant cell differentiation, altered gene regulatory networks, and changes to key pathways that promote microglia/oligodendrocyte differentiation. Our studies provide insight into interactions between genetic risk and epigenetic processes associated with divergent affiliative behavior and lack of positive sociability.
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Lee MJ, Hammouda MB, Miao W, Okafor A, Jin Y, Sun H, Jain V, Markovtsov V, Diao Y, Gregory SG, Zhang JY. UBE2N is essential for maintenance of skin homeostasis and suppression of inflammation. bioRxiv 2023:2023.12.01.569631. [PMID: 38105982 PMCID: PMC10723344 DOI: 10.1101/2023.12.01.569631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
UBE2N, a Lys63-ubiquitin conjugating enzyme, plays critical roles in embryogenesis and immune system development and function. However, its roles in adult epithelial tissue homeostasis and pathogenesis are unclear. We generated conditional mouse models that deleted Ube2n in skin cells in a temporally and spatially controlled manner. We found that Ube2n-knockout (KO) in the adult skin keratinocytes induced a range of inflammatory skin defects characteristic of psoriatic and actinic keratosis. These included eczematous inflammation, epidermal and dermal thickening, parakeratosis, and increased immune cell infiltration, as well as signs of edema and blistering. Single cell transcriptomic analyses and RT-qPCR showed that Ube2n KO keratinocytes expressed elevated myeloid cell chemo-attractants such as Cxcl1 and Cxcl2 and decreased the homeostatic T lymphocyte chemo-attractant, Ccl27a. Consistently, the infiltrating immune cells of Ube2n-KO skin were predominantly myeloid-derived cells including neutrophils and M1-like macrophages that were highly inflammatory, as indicated by expression of Il1β and Il24. Pharmacological blockade of the IL-1 receptor associated kinases (IRAK1/4) alleviated eczema, epidermal and dermal thickening, and immune infiltration of the Ube2n mutant skin. Together, these findings highlight a key role of keratinocyte-UBE2N in maintenance of epidermal homeostasis and skin immunity and identify IRAK1/4 as potential therapeutic target for inflammatory skin disorders.
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Affiliation(s)
- Min Jin Lee
- Department of Dermatology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | | | - Wanying Miao
- Department of Dermatology, Duke University, Durham, NC, USA
| | - Arinze Okafor
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Yingai Jin
- Department of Dermatology, Duke University, Durham, NC, USA
| | - Huiying Sun
- Department of Dermatology, Duke University, Durham, NC, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Durham, NC, USA
| | | | - Yarui Diao
- Department of Cell Biology, Duke University, Durham, NC, USA
| | | | - Jennifer Y Zhang
- Department of Dermatology, Duke University, Durham, NC, USA
- Department of Pathology, Duke University, Durham, NC, USA
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Mangoli A, Wu S, Liu HQ, Aksu M, Jain V, Foreman BE, Regal JA, Weidenhammer LB, Stewart CE, Guerra Garcia ME, Hocke E, Abramson K, Williams NT, Luo L, Deland K, Attardi L, Abe K, Hashizume R, Ashley DM, Becher OJ, Kirsch DG, Gregory SG, Reitman ZJ. Ataxia-telangiectasia mutated ( Atm ) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy. bioRxiv 2023:2023.10.18.562892. [PMID: 37904990 PMCID: PMC10614905 DOI: 10.1101/2023.10.18.562892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Diffuse midline gliomas (DMGs) are lethal brain tumors characterized by p53-inactivating mutations and oncohistone H3.3K27M mutations that rewire the cellular response to genotoxic stress, which presents therapeutic opportunities. We used RCAS/tv-a retroviruses and Cre recombinase to inactivate p53 and induce K27M in the native H3f3a allele in a lineage- and spatially-directed manner, yielding primary mouse DMGs. Genetic or pharmacologic disruption of the DNA damage response kinase Ataxia-telangiectasia mutated (ATM) enhanced the efficacy of focal brain irradiation, extending mouse survival. This finding suggests that targeting ATM will enhance the efficacy of radiation therapy for p53-mutant DMG but not p53-wildtype DMG. We used spatial in situ transcriptomics and an allelic series of primary murine DMG models with different p53 mutations to identify transactivation-independent p53 activity as a key mediator of such radiosensitivity. These studies deeply profile a genetically faithful and versatile model of a lethal brain tumor to identify resistance mechanisms for a therapeutic strategy currently in clinical trials.
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Chao AS, Matak P, Pegram K, Powers J, Hutson C, Jo R, Dubois L, Thompson JW, Smith PB, Jain V, Liu C, Younge NE, Rikard B, Reyes EY, Shinohara ML, Gregory SG, Goldberg RN, Benner EJ. 20-αHydroxycholesterol, an oxysterol in human breast milk, reverses mouse neonatal white matter injury through Gli-dependent oligodendrogenesis. Cell Stem Cell 2023; 30:1054-1071.e8. [PMID: 37541211 PMCID: PMC10625465 DOI: 10.1016/j.stem.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/21/2023] [Accepted: 07/12/2023] [Indexed: 08/06/2023]
Abstract
White matter injuries (WMIs) are the leading cause of neurologic impairment in infants born premature. There are no treatment options available. The most common forms of WMIs in infants occur prior to the onset of normal myelination, making its pathophysiology distinctive, thus requiring a tailored approach to treatment. Neonates present a unique opportunity to repair WMIs due to a transient abundance of neural stem/progenitor cells (NSPCs) present in the germinal matrix with oligodendrogenic potential. We identified an endogenous oxysterol, 20-αHydroxycholesterol (20HC), in human maternal breast milk that induces oligodendrogenesis through a sonic hedgehog (shh), Gli-dependent mechanism. Following WMI in neonatal mice, injection of 20HC induced subventricular zone-derived oligodendrogenesis and improved myelination in the periventricular white matter, resulting in improved motor outcomes. Targeting the oligodendrogenic potential of postnatal NSPCs in neonates with WMIs may be further developed into a novel approach to mitigate this devastating complication of preterm birth.
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Affiliation(s)
- Agnes S Chao
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Pavle Matak
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Kelly Pegram
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - James Powers
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Collin Hutson
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Rebecca Jo
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Laura Dubois
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Center for Genomics and Computational Biology, School of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - P Brian Smith
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Vaibhav Jain
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Chunlei Liu
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Noelle E Younge
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Blaire Rikard
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Estefany Y Reyes
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mari L Shinohara
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Simon G Gregory
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ronald N Goldberg
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA
| | - Eric J Benner
- Division of Neonatology, Department of Pediatrics, Duke University Medical Center, The Jean and George Brumley, Jr. Neonatal-Perinatal Institute, Durham, NC 27710, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA.
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Hirano M, Galarza-Muñoz G, Nagasawa C, Schott G, Wang L, Antonia AL, Jain V, Yu X, Widen SG, Briggs FBS, Gregory SG, Ko DC, Fagg WS, Bradrick S, Garcia-Blanco MA. The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate. eLife 2023; 12:e76927. [PMID: 37261960 PMCID: PMC10234631 DOI: 10.7554/elife.76927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/09/2023] [Indexed: 06/03/2023] Open
Abstract
Genes associated with increased susceptibility to multiple sclerosis (MS) have been identified, but their functions are incompletely understood. One of these genes codes for the RNA helicase DExD/H-Box Polypeptide 39B (DDX39B), which shows genetic and functional epistasis with interleukin-7 receptor-α gene (IL7R) in MS-risk. Based on evolutionary and functional arguments, we postulated that DDX39B enhances immune tolerance thereby decreasing MS risk. Consistent with such a role we show that DDX39B controls the expression of many MS susceptibility genes and important immune-related genes. Among these we identified Forkhead Box P3 (FOXP3), which codes for the master transcriptional factor in CD4+/CD25+ T regulatory cells. DDX39B knockdown led to loss of immune-regulatory and gain of immune-effector expression signatures. Splicing of FOXP3 introns, which belong to a previously unrecognized type of introns with C-rich polypyrimidine tracts, was exquisitely sensitive to DDX39B levels. Given the importance of FOXP3 in autoimmunity, this work cements DDX39B as an important guardian of immune tolerance.
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Affiliation(s)
- Minato Hirano
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- National Research Center for the Control and Prevention of Infectious Disease, Nagasaki UniversityNagasakiJapan
| | - Gaddiel Galarza-Muñoz
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Autoimmunity Biological SolutionsGalvestonUnited States
| | - Chloe Nagasawa
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Human Pathophysiology and Translational Medicine Program, Institute for Translational Sciences, University of Texas Medical BranchGalvestonUnited States
| | - Geraldine Schott
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke UniversityDurhamUnited States
| | - Xiaoying Yu
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Department of Preventive Medicine and Population Health, University of Texas Medical BranchGalvestonUnited States
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Farren BS Briggs
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve UniversityClevelandUnited States
| | - Simon G Gregory
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
- Duke Molecular Physiology Institute, Duke UniversityDurhamUnited States
- Department of Neurology, Duke University School of MedicineDurhamUnited States
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
- Division of Infectious Diseases, Department of Medicine, Duke UniversityDurhamUnited States
| | - William S Fagg
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Transplant Division, Department of Surgery, University of Texas Medical BranchGalvestonUnited States
| | - Shelton Bradrick
- Institute of Human Infections and Immunity, University of Texas Medical BranchGalvestonUnited States
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Department of Internal Medicine, University of Texas Medical BranchGalvestonUnited States
- Department of Microbiology, Immunology and Cancer Biology, University of VirginiaCharlottesvilleUnited States
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Allen JP, Danoff JS, Costello MA, Loeb EL, Davis AA, Hunt GL, Gregory SG, Giamberardino SN, Connelly JJ. Adolescent peer struggles predict accelerated epigenetic aging in midlife. Dev Psychopathol 2023; 35:912-925. [PMID: 35379374 PMCID: PMC9532470 DOI: 10.1017/s0954579422000153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study examined struggles to establish autonomy and relatedness with peers in adolescence and early adulthood as predictors of advanced epigenetic aging assessed at age 30. Participants (N = 154; 67 male and 87 female) were observed repeatedly, along with close friends and romantic partners, from ages 13 through 29. Observed difficulty establishing close friendships characterized by mutual autonomy and relatedness from ages 13 to 18, an interview-assessed attachment state of mind lacking autonomy and valuing of attachment at 24, and self-reported difficulties in social integration across adolescence and adulthood were all linked to greater epigenetic age at 30, after accounting for chronological age, gender, race, and income. Analyses assessing the unique and combined effects of these factors, along with lifetime history of cigarette smoking, indicated that each of these factors, except for adult social integration, contributed uniquely to explaining epigenetic age acceleration. Results are interpreted as evidence that the adolescent preoccupation with peer relationships may be highly functional given the relevance of such relationships to long-term physical outcomes.
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Regal JA, Guerra García ME, Jain V, Chandramohan V, Ashley DM, Gregory SG, Thompson EM, López GY, Reitman ZJ. Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population. Acta Neuropathol Commun 2023; 11:50. [PMID: 36966348 PMCID: PMC10039537 DOI: 10.1186/s40478-023-01548-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Gangliogliomas are brain tumors composed of neuron-like and macroglia-like components that occur in children and young adults. Gangliogliomas are often characterized by a rare population of immature astrocyte-appearing cells expressing CD34, a marker expressed in the neuroectoderm (neural precursor cells) during embryogenesis. New insights are needed to refine tumor classification and to identify therapeutic approaches. We evaluated five gangliogliomas with single nucleus RNA-seq, cellular indexing of transcriptomes and epitopes by sequencing, and/or spatially-resolved RNA-seq. We uncovered a population of CD34+ neoplastic cells with mixed neuroectodermal, immature astrocyte, and neuronal markers. Gene regulatory network interrogation in these neuroectoderm-like cells revealed control of transcriptional programming by TCF7L2/MEIS1-PAX6 and SOX2, similar to that found during neuroectodermal/neural development. Developmental trajectory analyses place neuroectoderm-like tumor cells as precursor cells that give rise to neuron-like and macroglia-like neoplastic cells. Spatially-resolved transcriptomics revealed a neuroectoderm-like tumor cell niche with relative lack of vascular and immune cells. We used these high resolution results to deconvolute clinically-annotated transcriptomic data, confirming that CD34+ cell-associated gene programs associate with gangliogliomas compared to other glial brain tumors. Together, these deep transcriptomic approaches characterized a ganglioglioma cellular hierarchy-confirming CD34+ neuroectoderm-like tumor precursor cells, controlling transcription programs, cell signaling, and associated immune cell states. These findings may guide tumor classification, diagnosis, prognostication, and therapeutic investigations.
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Affiliation(s)
- Joshua A Regal
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
| | | | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | | | - David M Ashley
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27710, USA
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| | - Giselle Y López
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
- Department of Pathology, Duke University, Durham, NC, 27710, USA
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA.
- Department of Neurosurgery, Duke University, Durham, NC, 27710, USA.
- Department of Pathology, Duke University, Durham, NC, 27710, USA.
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12
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Khatri A, Todd JL, Kelly FL, Nagler A, Ji Z, Jain V, Gregory SG, Weinhold KJ, Palmer SM. JAK-STAT activation contributes to cytotoxic T cell-mediated basal cell death in human chronic lung allograft dysfunction. JCI Insight 2023; 8:167082. [PMID: 36946463 PMCID: PMC10070100 DOI: 10.1172/jci.insight.167082] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/01/2023] [Indexed: 03/23/2023] Open
Abstract
Chronic lung allograft dysfunction (CLAD) is the leading cause of death in lung transplant recipients. CLAD is characterized clinically by a persistent decline in pulmonary function and histologically by the development of airway-centered fibrosis known as bronchiolitis obliterans. There are no approved therapies to treat CLAD, and the mechanisms underlying its development remain poorly understood. We performed single-cell RNA-Seq and spatial transcriptomic analysis of explanted tissues from human lung recipients with CLAD, and we performed independent validation studies to identify an important role of Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling in airway epithelial cells that contributes to airway-specific alloimmune injury. Specifically, we established that activation of JAK-STAT signaling leads to upregulation of major histocompatibility complex 1 (MHC-I) in airway basal cells, an important airway epithelial progenitor population, which leads to cytotoxic T cell-mediated basal cell death. This study provides mechanistic insight into the cell-to-cell interactions driving airway-centric alloimmune injury in CLAD, suggesting a potentially novel therapeutic strategy for CLAD prevention or treatment.
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Affiliation(s)
- Aaditya Khatri
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Jamie L Todd
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Fran L Kelly
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Andrew Nagler
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
- Department of Neurology, Duke University Medical Center, Durham, North Carolina, USA
| | - Kent J Weinhold
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Scott M Palmer
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
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Siecinski SK, Giamberardino SN, Spanos M, Hauser AC, Gibson JR, Chandrasekhar T, Trelles MDP, Rockhill CM, Palumbo ML, Cundiff AW, Montgomery A, Siper P, Minjarez M, Nowinski LA, Marler S, Kwee LC, Shuffrey LC, Alderman C, Weissman J, Zappone B, Mullett JE, Crosson H, Hong N, Luo S, She L, Bhapkar M, Dean R, Scheer A, Johnson JL, King BH, McDougle CJ, Sanders KB, Kim SJ, Kolevzon A, Veenstra-VanderWeele J, Hauser ER, Sikich L, Gregory SG. Genetic and epigenetic signatures associated with plasma oxytocin levels in children and adolescents with autism spectrum disorder. Autism Res 2023; 16:502-523. [PMID: 36609850 PMCID: PMC10023458 DOI: 10.1002/aur.2884] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023]
Abstract
Oxytocin (OT), the brain's most abundant neuropeptide, plays an important role in social salience and motivation. Clinical trials of the efficacy of OT in autism spectrum disorder (ASD) have reported mixed results due in part to ASD's complex etiology. We investigated whether genetic and epigenetic variation contribute to variable endogenous OT levels that modulate sensitivity to OT therapy. To carry out this analysis, we integrated genome-wide profiles of DNA-methylation, transcriptional activity, and genetic variation with plasma OT levels in 290 participants with ASD enrolled in a randomized controlled trial of OT. Our analysis identified genetic variants with novel association with plasma OT, several of which reside in known ASD risk genes. We also show subtle but statistically significant association of plasma OT levels with peripheral transcriptional activity and DNA-methylation profiles across several annotated gene sets. These findings broaden our understanding of the effects of the peripheral oxytocin system and provide novel genetic candidates for future studies to decode the complex etiology of ASD and its interaction with OT signaling and OT-based interventions. LAY SUMMARY: Oxytocin (OT) is an abundant chemical produced by neurons that plays an important role in social interaction and motivation. We investigated whether genetic and epigenetic factors contribute to variable OT levels in the blood. To this, we integrated genetic, gene expression, and non-DNA regulated (epigenetic) signatures with blood OT levels in 290 participants with autism enrolled in an OT clinical trial. We identified genetic association with plasma OT, several of which reside in known autism risk genes. We also show statistically significant association of plasma OT levels with gene expression and epigenetic across several gene pathways. These findings broaden our understanding of the factors that influence OT levels in the blood for future studies to decode the complex presentation of autism and its interaction with OT and OT-based treatment.
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Affiliation(s)
- Stephen K Siecinski
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Marina Spanos
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Annalise C Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tara Chandrasekhar
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - M D Pilar Trelles
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol M Rockhill
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Michelle L Palumbo
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Paige Siper
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mendy Minjarez
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Lisa A Nowinski
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sarah Marler
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Lydia C Kwee
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Cheryl Alderman
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jordana Weissman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brooke Zappone
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Jennifer E Mullett
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hope Crosson
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Natalie Hong
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Sheng Luo
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Lilin She
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Manjushri Bhapkar
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Russell Dean
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abby Scheer
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jacqueline L Johnson
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bryan H King
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Christopher J McDougle
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin B Sanders
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Soo-Jeong Kim
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Alexander Kolevzon
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Linmarie Sikich
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
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Xie S, Choudhari S, Wu CL, Abramson K, Corcoran D, Gregory SG, Thimmapuram J, Guilak F, Little D. Aging and obesity prime the methylome and transcriptome of adipose stem cells for disease and dysfunction. FASEB J 2023; 37:e22785. [PMID: 36794668 PMCID: PMC10561192 DOI: 10.1096/fj.202201413r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023]
Abstract
The epigenome of stem cells occupies a critical interface between genes and environment, serving to regulate expression through modification by intrinsic and extrinsic factors. We hypothesized that aging and obesity, which represent major risk factors for a variety of diseases, synergistically modify the epigenome of adult adipose stem cells (ASCs). Using integrated RNA- and targeted bisulfite-sequencing in murine ASCs from lean and obese mice at 5- and 12-months of age, we identified global DNA hypomethylation with either aging or obesity, and a synergistic effect of aging combined with obesity. The transcriptome of ASCs in lean mice was relatively stable to the effects of age, but this was not true in obese mice. Functional pathway analyses identified a subset of genes with critical roles in progenitors and in diseases of obesity and aging. Specifically, Mapt, Nr3c2, App, and Ctnnb1 emerged as potential hypomethylated upstream regulators in both aging and obesity (AL vs. YL and AO vs. YO), and App, Ctnnb1, Hipk2, Id2, and Tp53 exhibited additional effects of aging in obese animals. Furthermore, Foxo3 and Ccnd1 were potential hypermethylated upstream regulators of healthy aging (AL vs. YL), and of the effects of obesity in young animals (YO vs. YL), suggesting that these factors could play a role in accelerated aging with obesity. Finally, we identified candidate driver genes that appeared recurrently in all analyses and comparisons undertaken. Further mechanistic studies are needed to validate the roles of these genes capable of priming ASCs for dysfunction in aging- and obesity-associated pathologies.
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Affiliation(s)
- Shaojun Xie
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
| | - Sulbha Choudhari
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
- Advanced Biomedical Computational Science, Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research, 8560 Progress Drive, Frederick, MD 2170
| | - Chia-Lung Wu
- Department of Orthopaedics and Rehabilitation, Center for Musculoskeletal Research, University of Rochester, Rochester, NY, 14611
| | - Karen Abramson
- Duke Molecular Physiology Institute, 300 North Duke Street, Durham, NC 27701
| | - David Corcoran
- Genomic Analysis and Bioinformatics Shared Resource, Duke Center for Genomic and Computational Biology, 101 Science Drive, Duke University Medical Center Box 3382, Durham, NC 27708
- Lineberger Bioinformatics Core, 5200 Marsico Hall, University of North Carolina-Chapel Hill, Chapel Hill, NC 27516
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, 300 North Duke Street, Durham, NC 27701
- Department of Neurology, Duke University School of Medicine, 311 Research Drive, Durham, NC 27710
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, 1022 Young Hall, 155 S. Grant Street, West Lafayette, IN 47907
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University in St. Louis, 4515 McKinley Ave., St. Louis, MO 63110
- Shriners Hospitals for Children – St. Louis, 4400 Clayton Ave, St. Louis Missouri 63110
| | - Dianne Little
- Departments of Basic Medical Sciences and Biomedical Engineering, Purdue University, 2186 Lynn Hall, 625 Harrison St, West Lafayette, IN 47907-2026
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15
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Schott BH, Wang L, Zhu X, Harding AT, Ko ER, Bourgeois JS, Washington EJ, Burke TW, Anderson J, Bergstrom E, Gardener Z, Paterson S, Brennan RG, Chiu C, McClain MT, Woods CW, Gregory SG, Heaton NS, Ko DC. Single-cell genome-wide association reveals that a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. Cell Genom 2022; 2:100207. [PMID: 36465279 PMCID: PMC9718543 DOI: 10.1016/j.xgen.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
During pandemics, individuals exhibit differences in risk and clinical outcomes. Here, we developed single-cell high-throughput human in vitro susceptibility testing (scHi-HOST), a method for rapidly identifying genetic variants that confer resistance and susceptibility. We applied this method to influenza A virus (IAV), the cause of four pandemics since the start of the 20th century. scHi-HOST leverages single-cell RNA sequencing (scRNA-seq) to simultaneously assign genetic identity to cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral burden, and identify expression quantitative trait loci. Integration of scHi-HOST with human challenge and experimental validation demonstrated that a missense variant in endoplasmic reticulum aminopeptidase 1 (ERAP1; rs27895) increased IAV burden in cells and human volunteers. rs27895 exhibits population differentiation, likely contributing to greater permissivity of cells from African populations to IAV. scHi-HOST is a broadly applicable method and resource for decoding infectious-disease genetics.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- These authors contributed equally
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- These authors contributed equally
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Hospital Medicine, Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Durham, NC 27705, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Jack Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Emma Bergstrom
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Zoe Gardener
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Suzanna Paterson
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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16
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Zhang J, Zimmermann B, Galletti G, Halabi S, Gjyrezi A, Yang Q, Gupta S, Verma A, Sboner A, Anand M, George DJ, Gregory SG, Mahtani P, Hong S, Pascual V, Mavragani CP, Antonarakis ES, Nanus DM, Tagawa ST, Elemento O, Armstrong AJ, Giannakakou P. Abstract 646: Liquid biopsy transcriptomics identify pathways associated with poor outcomes and immune phenotypes in men with mCRPC. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-646] [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
Androgen receptor signaling inhibitors (ARSi) and taxanes are mainstays for patients with metastatic castration-resistant prostate cancer (mCRPC). However, patient response is heterogeneous, and the molecular underpinnings of treatment resistance are not well elucidated.
To identify clinically meaningful mechanisms of treatment resistance, we performed transcriptome analysis of circulating tumor cells (CTCs) isolated from mCRPC patients enrolled in two independent prospective clinical trials: PROPHECY, a clinical study of patients (n=118) treated with abiraterone or enzalutamide followed by docetaxel; and TAXYNERGY where patients were randomized to docetaxel or cabazitaxel treatment. CTCs were obtained at baseline (before treatment), on treatment and at progression and their comprehensive transcriptomic analysis was correlated with clinical outcomes. To uncover potential involvement of the circulating immune macroenvironment (CIME) in treatment resistance, we performed transcriptomic analysis of matching peripheral blood mononuclear cells (PBMCs) using an established, rigorous, blood-derived transcriptional modular framework.
In PROPHECY, CTC RNA-seq identified that RB loss concurrently with enhanced E2F signaling networks were associated with intrinsic ARSi resistance. Using single sample GSEA (ssGSEA) score, we identified that the RB/E2F common signature at baseline was associated with short PFS (median PFS=6.5 months) and OS (median OS=24.5 months) (hazard ratio (HR) = 3.5; 95% CI 1.5-8.2) in men with mCRPC. We further developed a BRCA-loss transcriptional signature, and validated it in the SU2C mCRPC patient cohort, expanding the identification of patients with BRCA-loss phenotypes beyond genomic loss. Applying this signature to PROPHECY baseline samples, we showed that men with high BRCA-loss scores experienced shorter OS (HR=2.42; 95% CI=1-5.9). Through the comparison of CTC transcriptomic profiles at progression with baseline, we identified an inflammatory response signature in CTCs which was significantly associated with acquired ARSi resistance. Transcriptomic PBMC analysis further identified enrichment of inflammasome gene signatures at progression, with concurrent downregulation of CD8+ T and NK cells.
Furthermore, preliminary data from both clinical trials, showed a significant upregulation of TGF-β1 and corresponding TGFβ-Receptor signaling pathway in CTCs from patients at progression following taxane treatment, suggesting a role for TGFβ pathway in clinical response to taxane chemotherapy.
Taken together, these data demonstrate that liquid biopsy transcriptomics of both tumor cells and immune cells can identify molecular pathways associated with treatment resistance paving the way for treatment optimization and the development of novel precision therapies in patients with mCRPC.
Citation Format: Jiaren Zhang, Bob Zimmermann, Giuseppe Galletti, Susan Halabi, Ada Gjyrezi, Qian Yang, Santosh Gupta, Akanksha Verma, Andrea Sboner, Monika Anand, Daniel J. George, Simon G. Gregory, Prerna Mahtani, Seunghee Hong, Virginia Pascual, Clio P. Mavragani, Emmanuel S. Antonarakis, David M. Nanus, Scott T. Tagawa, Olivier Elemento, Andrew J. Armstrong, Paraskevi Giannakakou. Liquid biopsy transcriptomics identify pathways associated with poor outcomes and immune phenotypes in men with mCRPC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 646.
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Abstract
Human red blood cells (RBCs), or erythrocytes, are the most abundant blood cells responsible for gas exchange. RBC diseases affect hundreds of millions of people and impose enormous financial and personal burdens. One well-recognized, but poorly understood feature of RBC populations within the same individual are their phenotypic heterogeneity. The granular characterization of phenotypic RBC variation in normative and disease states may allow us to identify the genetic determinants of red cell diseases and reveal novel therapeutic approaches for their treatment. Previously, we discovered diverse RNA transcripts in RBCs that has allowed us to dissect the phenotypic heterogeneity and malaria resistance of sickle red cells. However, these analyses failed to capture the heterogeneity found in RBC sub-populations. To overcome this limitation, we have performed single cell RNA-Seq to analyze the transcriptional heterogeneity of RBCs from three adult healthy donors which have been stored in the blood bank conditions and assayed at day 1 and day 15. The expression pattern clearly separated RBCs into seven distinct clusters that include one RBC cluster that expresses HBG2 and a small population of RBCs that express fetal hemoglobin (HbF) that we annotated as F cells. Almost all HBG2-expessing cells also express HBB, suggesting bi-allelic expression in single RBC from the HBG2/HBB loci, and we annotated another cluster as reticulocytes based on canonical gene expression. Additional RBC clusters were also annotated based on the enriched expression of NIX, ACVR2B and HEMGN, previously shown to be involved in erythropoiesis. Finally, we found the storage of RBC was associated with an increase in the ACVR2B and F-cell clusters. Collectively, these data indicate the power of single RBC RNA-Seq to capture and discover known and unexpected heterogeneity of RBC population.
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Affiliation(s)
- Vaibhav Jain
- Department of Neurology, Durham, NC, United States.,Duke Molecular Physiology Institute, Durham, NC, United States
| | - Wen-Hsuan Yang
- Department of Molecular Genetics and Microbiology, Durham, NC, United States.,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, United States
| | - Jianli Wu
- Department of Molecular Genetics and Microbiology, Durham, NC, United States.,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, United States
| | - John D Roback
- Center for Transfusion and Cellular Therapies, Durham, NC, United States.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Simon G Gregory
- Department of Neurology, Durham, NC, United States.,Duke Molecular Physiology Institute, Durham, NC, United States
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Durham, NC, United States.,Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, United States
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Dungan JR, Qin X, Gregory SG, Cooper-Dehoff R, Duarte JD, Qin H, Gulati M, Taylor JY, Pepine CJ, Hauser ER, Kraus WE. Sex-dimorphic gene effects on survival outcomes in people with coronary artery disease. American Heart Journal Plus: Cardiology Research and Practice 2022; 17. [PMID: 35959094 PMCID: PMC9365120 DOI: 10.1016/j.ahjo.2022.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Ischemic coronary heart disease (IHD) is the leading cause of death worldwide. Genetic variation is presumed to be a major factor underlying sex differences for IHD events, including mortality. The purpose of this study was to identify sex-specific candidate genes associated with all-cause mortality among people diagnosed with coronary artery disease (CAD). Methods: We performed a sex-stratified, exploratory genome-wide association (GWAS) screen using existing data from CAD-diagnosed males (n = 510) and females (n = 174) who reported European ancestry from the Duke Catheterization Genetics biorepository. Extant genotype data for 785,945 autosomal SNPs generated with the Human Omni1-Quad BeadChip (Illumina, CA, USA) were analyzed using an additive inheritance model. We estimated instantaneous risk of all-cause mortality by genotype groups across the 11-year follow-up using Cox multivariate regression, covarying for age and genomic ancestry. Results: The top GWAS hits associated with all-cause mortality among people with CAD included 8 SNPs among males and 15 among females (p = 1 × 10−6 or 10−7), adjusted for covariates. Cross-sex comparisons revealed distinct candidate genes. Biologically relevant candidates included rs9932462 (EMP2/TEKT5) and rs2835913 (KCNJ6) among males and rs7217169 (RAP1GAP2), rs8021816 (PRKD1), rs8133010 (PDE9A), and rs12145981 (LPGAT1) among females. Conclusions: We report 20 sex-specific candidate genes having suggestive association with all-cause mortality among CAD-diagnosed subjects. Findings demonstrate proof of principle for identifying sex-associated genetic factors that may help explain differential mortality risk in people with CAD. Replication and meta-analyses in larger studies with more diverse samples will strengthen future work in this area.
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Allen JP, Danoff JS, Costello MA, Hunt GL, Hellwig AF, Krol KM, Gregory SG, Giamberardino SN, Sugden K, Connelly JJ. Lifetime marijuana use and epigenetic age acceleration: A 17-year prospective examination. Drug Alcohol Depend 2022; 233:109363. [PMID: 35231715 PMCID: PMC8982677 DOI: 10.1016/j.drugalcdep.2022.109363] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/19/2022] [Accepted: 02/15/2022] [Indexed: 12/12/2022]
Abstract
AIMS This study was designed to assess links between lifetime levels of marijuana use and accelerated epigenetic aging. DESIGN Prospective longitudinal study, following participants annually from age 13 to age 30. SETTING AND PARTICIPANTS A community sample of 154 participants recruited from a small city in the Southeastern United States. MEASUREMENTS Participants completed annual assessments of marijuana use from age 13 to age 29 and provided blood samples that yielded two indices of epigenetic aging (DNAmGrimAge and DunedinPoAm) at age 30. Additional covariates examined included history of cigarette smoking, anxiety and depressive symptoms, childhood illness, gender, adolescent-era family income, and racial/ethnic minority status. FINDINGS Lifetime marijuana use predicted accelerated epigenetic aging, with effects remaining even after covarying cell counts, demographic factors and chronological age (β's = 0.32 & 0.27, p's < 0.001, 95% CI's = 0.21-0.43 & 0.16-0.39 for DNAmGrimAge and DunedinPoAm, respectively). Predictions remained after accounting for cigarette smoking (β's = 0.25 & 0.21, respectively, p's < 0.001, 95% CI's = 0.14-0.37 & 0.09-0.32 for DNAmGrimAge and DunedinPoAm, respectively). A dose-response effect was observed and there was also evidence that effects were dependent upon recency of use. Effects of marijuana use appeared to be fully mediated by hypomethylation of a site linked to effects of hydrocarbon inhalation (cg05575921). CONCLUSIONS Marijuana use predicted epigenetic changes linked to accelerated aging, with evidence suggesting that effects may be primarily due to hydrocarbon inhalation among marijuana smokers. Further research is warranted to explore mechanisms underlying this linkage.
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20
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SoRelle ED, Dai J, Bonglack EN, Heckenberg EM, Zhou JY, Giamberardino SN, Bailey JA, Gregory SG, Chan C, Luftig MA. Correction: Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines. eLife 2021; 10:75422. [PMID: 34762045 PMCID: PMC8585475 DOI: 10.7554/elife.75422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/30/2022] Open
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21
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Sikich L, Kolevzon A, King BH, McDougle CJ, Sanders KB, Kim SJ, Spanos M, Chandrasekhar T, Trelles MDP, Rockhill CM, Palumbo ML, Witters Cundiff A, Montgomery A, Siper P, Minjarez M, Nowinski LA, Marler S, Shuffrey LC, Alderman C, Weissman J, Zappone B, Mullett JE, Crosson H, Hong N, Siecinski SK, Giamberardino SN, Luo S, She L, Bhapkar M, Dean R, Scheer A, Johnson JL, Gregory SG, Veenstra-VanderWeele J. Intranasal Oxytocin in Children and Adolescents with Autism Spectrum Disorder. N Engl J Med 2021; 385:1462-1473. [PMID: 34644471 PMCID: PMC9701092 DOI: 10.1056/nejmoa2103583] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Experimental studies and small clinical trials have suggested that treatment with intranasal oxytocin may reduce social impairment in persons with autism spectrum disorder. Oxytocin has been administered in clinical practice to many children with autism spectrum disorder. METHODS We conducted a 24-week, placebo-controlled phase 2 trial of intranasal oxytocin therapy in children and adolescents 3 to 17 years of age with autism spectrum disorder. Participants were randomly assigned in a 1:1 ratio, with stratification according to age and verbal fluency, to receive oxytocin or placebo, administered intranasally, with a total target dose of 48 international units daily. The primary outcome was the least-squares mean change from baseline on the Aberrant Behavior Checklist modified Social Withdrawal subscale (ABC-mSW), which includes 13 items (scores range from 0 to 39, with higher scores indicating less social interaction). Secondary outcomes included two additional measures of social function and an abbreviated measure of IQ. RESULTS Of the 355 children and adolescents who underwent screening, 290 were enrolled. A total of 146 participants were assigned to the oxytocin group and 144 to the placebo group; 139 and 138 participants, respectively, completed both the baseline and at least one postbaseline ABC-mSW assessments and were included in the modified intention-to-treat analyses. The least-squares mean change from baseline in the ABC-mSW score (primary outcome) was -3.7 in the oxytocin group and -3.5 in the placebo group (least-squares mean difference, -0.2; 95% confidence interval, -1.5 to 1.0; P = 0.61). Secondary outcomes generally did not differ between the trial groups. The incidence and severity of adverse events were similar in the two groups. CONCLUSIONS This placebo-controlled trial of intranasal oxytocin therapy in children and adolescents with autism spectrum disorder showed no significant between-group differences in the least-squares mean change from baseline on measures of social or cognitive functioning over a period of 24 weeks. (Funded by the National Institute of Child Health and Human Development; SOARS-B ClinicalTrials.gov number, NCT01944046.).
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Affiliation(s)
- Linmarie Sikich
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Alexander Kolevzon
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Bryan H King
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Christopher J McDougle
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Kevin B Sanders
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Soo-Jeong Kim
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Marina Spanos
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Tara Chandrasekhar
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - M D Pilar Trelles
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Carol M Rockhill
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Michelle L Palumbo
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Allyson Witters Cundiff
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Alicia Montgomery
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Paige Siper
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Mendy Minjarez
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Lisa A Nowinski
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Sarah Marler
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Lauren C Shuffrey
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Cheryl Alderman
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Jordana Weissman
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Brooke Zappone
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Jennifer E Mullett
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Hope Crosson
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Natalie Hong
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Stephen K Siecinski
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Stephanie N Giamberardino
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Sheng Luo
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Lilin She
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Manjushri Bhapkar
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Russell Dean
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Abby Scheer
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Jacqueline L Johnson
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Simon G Gregory
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
| | - Jeremy Veenstra-VanderWeele
- From the Department of Psychiatry and Behavioral Sciences (L. Sikich, M.S., T.C., C.A., A.S.), the Duke Clinical Research Institute (L. Sikich, C.A., S.L., L. She, M.B.), the Duke Molecular Physiology Institute (S.K.S., S.N.G., S.G.G.), and the Departments of Biostatistics and Bioinformatics (S.L.) and Neurology (S.G.G.), Duke University, Durham, the Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill (L. Sikich, M.S., T.C., C.A., R.D., A.S., J.L.J.), and SAS Institute, Cary (J.L.J.) - all in North Carolina; the Department of Psychiatry, Icahn School of Medicine at Mount Sinai (A.K., M.D.P.T., P.S., J.W.), the Department of Psychiatry, Columbia University (A.M., L.C.S., N.H., J.V.-V.), and New York State Psychiatric Institute (J.V.-V.), New York, and the Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains (J.V.-V.) - all in New York; the Department of Psychiatry, University of California San Francisco, San Francisco (B.H.K.); the Department of Psychiatry, Seattle Children's Hospital and the University of Washington, Seattle (B.H.K., S.-J.K., C.M.R., M.M., B.Z.); the Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston (C.J.M., M.L.P., L.A.N., J.E.M.), and the Lurie Center for Autism, Lexington (C.J.M., M.L.P., L.A.N., J.E.M.) - all in Massachusetts; Hoffmann-La Roche, Basel, Switzerland (K.B.S.); the Department of Psychiatry, Vanderbilt University, Nashville (K.B.S., A.W.C., S.M., H.C.); the University of New South Wales, Sydney (A.M.); and Florida International University, Miami (N.H.)
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22
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Mariottoni P, Jiang SW, Prestwood CA, Jain V, Suwanpradid J, Whitley MJ, Coates M, Brown DA, Erdmann D, Corcoran DL, Gregory SG, Jaleel T, Zhang JY, Harris-Tryon TA, MacLeod AS. Single-Cell RNA Sequencing Reveals Cellular and Transcriptional Changes Associated With M1 Macrophage Polarization in Hidradenitis Suppurativa. Front Med (Lausanne) 2021; 8:665873. [PMID: 34504848 PMCID: PMC8421606 DOI: 10.3389/fmed.2021.665873] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/09/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by recurrent abscesses, nodules, and sinus tracts in areas of high hair follicle and sweat gland density. These sinus tracts can present with purulent drainage and scar formation. Dysregulation of multiple immune pathways drives the complexity of HS pathogenesis and may account for the heterogeneity of treatment response in HS patients. Using transcriptomic approaches, including single-cell sequencing and protein analysis, we here characterize the innate inflammatory landscape of HS lesions. We identified a shared upregulation of genes involved in interferon (IFN) and antimicrobial defense signaling through transcriptomic overlap analysis of differentially expressed genes (DEGs) in datasets from HS skin, diabetic foot ulcers (DFUs), and the inflammatory stage of normal healing wounds. Overlap analysis between HS- and DFU-specific DEGs revealed an enrichment of gene signatures associated with monocyte/macrophage functions. Single-cell RNA sequencing further revealed monocytes/macrophages with polarization toward a pro-inflammatory M1-like phenotype and increased effector function, including antiviral immunity, phagocytosis, respiratory burst, and antibody-dependent cellular cytotoxicity. Specifically, we identified the STAT1/IFN-signaling axis and the associated IFN-stimulated genes as central players in monocyte/macrophage dysregulation. Our data indicate that monocytes/macrophages are a potential pivotal player in HS pathogenesis and their pathways may serve as therapeutic targets and biomarkers in HS treatment.
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Affiliation(s)
- Paula Mariottoni
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
| | - Simon W. Jiang
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
| | - Courtney A. Prestwood
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke University, Durham, NC, United States
| | - Jutamas Suwanpradid
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
| | - Melodi Javid Whitley
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
| | - Margaret Coates
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
| | - David A. Brown
- Division of Plastic, Maxillofacial, and Oral Surgery, Duke University Medical Center, Durham, NC, United States
| | - Detlev Erdmann
- Division of Plastic, Maxillofacial, and Oral Surgery, Duke University Medical Center, Durham, NC, United States
| | - David L. Corcoran
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, United States
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC, United States
- Department of Neurology, Duke University School of Medicine, Durham, NC, United States
| | - Tarannum Jaleel
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
| | - Jennifer Y. Zhang
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
| | - Tamia A. Harris-Tryon
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Amanda S. MacLeod
- Department of Dermatology, School of Medicine, Duke University, Durham, NC, United States
- Department of Immunology, Duke University, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, United States
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23
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Brown LC, Halabi S, Schonhoft JD, Yang Q, Luo J, Nanus DM, Giannakakou P, Szmulewitz RZ, Danila DC, Barnett ES, Carbone EA, Zhao JL, Healy P, Anand M, Gill A, Jendrisak A, Berry WR, Gupta S, Gregory SG, Wenstrup R, Antonarakis ES, George DJ, Scher HI, Armstrong AJ. Circulating Tumor Cell Chromosomal Instability and Neuroendocrine Phenotype by Immunomorphology and Poor Outcomes in Men with mCRPC Treated with Abiraterone or Enzalutamide. Clin Cancer Res 2021; 27:4077-4088. [PMID: 33820782 DOI: 10.1158/1078-0432.ccr-20-3471] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/07/2020] [Accepted: 03/31/2021] [Indexed: 12/15/2022]
Abstract
PURPOSE While the detection of AR-V7 in circulating tumor cells (CTC) is associated with resistance to abiraterone or enzalutamide in men with metastatic castration-resistant prostate cancer (mCRPC), it only accounts for a minority of this resistance. Neuroendocrine (NE) differentiation or chromosomal instability (CIN) may be additional mechanisms that mediate resistance. EXPERIMENTAL DESIGN PROPHECY was a multicenter prospective study of men with high-risk mCRPC starting abiraterone or enzalutamide. A secondary objective was to assess Epic CTC CIN and NE phenotypes before abiraterone or enzalutamide and at progression. The proportional hazards (PH) model was used to investigate the prognostic importance of CIN and NE in predicting progression-free survival and overall survival (OS) adjusting for CTC number (CellSearch), AR-V7, prior therapy, and clinical risk score. The PH model was utilized to validate this association of NE with OS in an external dataset of patients treated similarly at Memorial Sloan Kettering Cancer Center (MSKCC; New York, NY). RESULTS We enrolled 118 men with mCRPC starting on abiraterone or enzalutamide; 107 were evaluable on the Epic platform. Of these, 36.4% and 8.4% were CIN positive and NE positive, respectively. CIN and NE were independently associated with worse OS [HR, 2.2; 95% confidence interval (CI), 1.2-4.0 and HR 3.8; 95% CI, 1.2-12.3, respectively] when treated with abiraterone/enzalutamide. The prognostic significance of NE positivity for worse OS was confirmed in the MSKCC dataset (n = 173; HR, 5.7; 95% CI, 2.6-12.7). CONCLUSIONS A high CIN and NE CTC phenotype is independently associated with worse survival in men with mCRPC treated with abiraterone/enzalutamide, warranting further prospective controlled predictive studies to inform treatment decisions.
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Affiliation(s)
- Landon C Brown
- Department of Medicine, Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Susan Halabi
- Department of Medicine, Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Duke University, Durham, North Carolina
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | | | - Qian Yang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Jun Luo
- Department of Urology, Johns Hopkins University, Baltimore, Maryland
| | | | | | | | - Daniel C Danila
- Weill Cornell Medical College, New York, New York
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Jimmy L Zhao
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Monika Anand
- Department of Medicine, Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Duke University, Durham, North Carolina
| | | | | | - William R Berry
- Department of Medicine, Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Santosh Gupta
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | | | | | - Daniel J George
- Department of Medicine, Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Howard I Scher
- Weill Cornell Medical College, New York, New York
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew J Armstrong
- Department of Medicine, Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Duke University, Durham, North Carolina.
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24
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Cronan MR, Hughes EJ, Brewer WJ, Viswanathan G, Hunt EG, Singh B, Mehra S, Oehlers SH, Gregory SG, Kaushal D, Tobin DM. A non-canonical type 2 immune response coordinates tuberculous granuloma formation and epithelialization. Cell 2021; 184:1757-1774.e14. [PMID: 33761328 PMCID: PMC8055144 DOI: 10.1016/j.cell.2021.02.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
The central pathogen-immune interface in tuberculosis is the granuloma, a complex host immune structure that dictates infection trajectory and physiology. Granuloma macrophages undergo a dramatic transition in which entire epithelial modules are induced and define granuloma architecture. In tuberculosis, relatively little is known about the host signals that trigger this transition. Using the zebrafish-Mycobacterium marinum model, we identify the basis of granuloma macrophage transformation. Single-cell RNA-sequencing analysis of zebrafish granulomas and analysis of Mycobacterium tuberculosis-infected macaques reveal that, even in the presence of robust type 1 immune responses, countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling, mediated via stat6, is absolutely required for epithelialization and granuloma formation. In mixed chimeras, stat6 acts cell autonomously within macrophages, where it is required for epithelioid transformation and incorporation into necrotic granulomas. These findings establish the signaling pathway that produces the hallmark structure of mycobacterial infection.
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MESH Headings
- Animals
- Animals, Genetically Modified/genetics
- Animals, Genetically Modified/metabolism
- Cadherins/genetics
- Cadherins/metabolism
- Cell Differentiation
- Disease Models, Animal
- Epithelioid Cells/cytology
- Epithelioid Cells/immunology
- Epithelioid Cells/metabolism
- Granuloma/immunology
- Granuloma/metabolism
- Granuloma/pathology
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/metabolism
- Immunity/physiology
- Interferon-gamma/metabolism
- Interleukin-12/metabolism
- Macrophages/cytology
- Macrophages/immunology
- Macrophages/metabolism
- Mycobacterium Infections, Nontuberculous/immunology
- Mycobacterium Infections, Nontuberculous/pathology
- Mycobacterium marinum/isolation & purification
- Mycobacterium marinum/physiology
- Necrosis
- Receptors, Interleukin-4/antagonists & inhibitors
- Receptors, Interleukin-4/genetics
- Receptors, Interleukin-4/metabolism
- STAT6 Transcription Factor/antagonists & inhibitors
- STAT6 Transcription Factor/genetics
- STAT6 Transcription Factor/metabolism
- Signal Transduction
- Zebrafish/growth & development
- Zebrafish/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Mark R Cronan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Erika J Hughes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Jared Brewer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Emily G Hunt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bindu Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Smriti Mehra
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Stefan H Oehlers
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Camperdown, NSW, Australia; The University of Sydney, Faculty of Medicine and Health & Marie Bashir Institute, Camperdown, NSW, Australia
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27710, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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25
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Gupta S, Halabi S, Kemeny G, Anand M, Giannakakou P, Nanus DM, George DJ, Gregory SG, Armstrong AJ. Circulating Tumor Cell Genomic Evolution and Hormone Therapy Outcomes in Men with Metastatic Castration-Resistant Prostate Cancer. Mol Cancer Res 2021; 19:1040-1050. [PMID: 33771885 DOI: 10.1158/1541-7786.mcr-20-0975] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/11/2021] [Accepted: 03/01/2021] [Indexed: 01/24/2023]
Abstract
Men with circulating tumor cell (CTC) AR-V7-positive metastatic castration-resistant prostate cancer (mCRPC) have worse outcomes when treated with enzalutamide/abiraterone. However, most men lack CTC AR-V7 detection, and additional predictive biomarkers are needed. We conducted a retrospective secondary analysis of the prospective PROPHECY trial (NCT02269982) of men with mCRPC undergoing treatment with enzalutamide/abiraterone, analyzing pooled CTC and germline DNA for whole-genome copy-number alterations (CNA) in 73 samples from 48 men over time along with pooled CTC and germline whole-exome sequencing on 22 paired samples before and following progression on androgen receptor (AR) inhibitor therapy to identify somatic genomic alterations associated with acquired resistance. We observed broad interpatient and longitudinal CTC genomic heterogeneity from AR-V7-negative men with mCRPC, including common gains of KDM6A, MYCN, and AR, and loss of ZFHX3, BRCA1, and PTEN. Men who had progression-free survival of ≤3 months despite enzalutamide/abiraterone treatment were more likely to have baseline CTC genomic loss of CHD1, PTEN, PHLPP1, and ZFHX3 and gains of BRCA2, KDM5D, MYCN, and SPARC. After progression on abiraterone/enzalutamide, we observed clonal evolution of CTCs harboring TP53 mutations and gain of ATM, KDM6A, and MYC, and loss of NCOR1, PTEN, RB1, and RUNX2. CTC genomic findings were independently confirmed in a separate cohort of mCRPC men who progressed despite prior treatment with abiraterone/enzalutamide (NCT02204943). IMPLICATIONS: We identified common and reproducible genomic alterations in CTCs from AR-V7-negative mCRPC men associated with poor outcomes during enzalutamide/abiraterone treatment, including CNAs in genes linked to lineage plasticity and epigenetic signaling, DNA repair, AR, TP53/RB1, PTEN, and WNT pathways.
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Affiliation(s)
- Santosh Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolin.,Epic Sciences, San Diego, California
| | - Susan Halabi
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Gabor Kemeny
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Monika Anand
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | | | - David M Nanus
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Daniel J George
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Departments of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Simon G Gregory
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolin
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina. .,Departments of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
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26
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Schott G, Galarza-Muñoz G, Trevino N, Chen X, Weirauch M, Gregory SG, Bradrick SS, Garcia-Blanco MA. U2AF2 binds IL7R exon 6 ectopically and represses its inclusion. RNA 2021; 27:rna.078279.120. [PMID: 33568552 PMCID: PMC8051268 DOI: 10.1261/rna.078279.120] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/02/2021] [Indexed: 06/03/2023]
Abstract
Interleukin 7 receptor α-chain is crucial for the development and maintenance of T cells and is genetically associated with autoimmune disorders including multiple sclerosis (MS), a demyelinating disease of the CNS. Exon 6 of IL7R encodes for the transmembrane domain of the receptor and is regulated by alternative splicing: inclusion or skipping of IL7R exon 6 results in membrane-bound or soluble IL7R isoforms, respectively. We previously identified a SNP (rs6897932) in IL7R exon 6, strongly associated with MS risk and showed that the risk allele (C) increases skipping of the exon, resulting in elevated levels of sIL7R. This has important pathological consequences as elevated levels of sIL7R has been shown to exacerbate the disease in the experimental autoimmune encephalomyelitis mouse model of MS. Understanding the regulation of exon 6 splicing provides important mechanistic insights into the pathogenesis of MS. Here we report two mechanisms by which IL7R exon 6 is controlled. First, a competition between PTBP1 and U2AF2 at the polypyrimidine tract (PPT) of intron 5, and second, an unexpected U2AF2-mediated assembly of spicing factors in the exon. We noted the presence of a branchpoint sequence (BPS) (TACTAAT or TACTAAC) within exon 6, which is stronger with the C allele. We also noted that the BPS is followed by a PPT and conjectured that silencing could be mediated by the binding of U2AF2 to that tract. In support of this model, we show that evolutionary conservation of the exonic PPT correlates well with the degree of alternative splicing of exon 6 in two non-human primate species and that U2AF2 binding to this PPT recruits U2 snRNP components to the exon. These observations provide the first explanation for the stronger silencing of IL7R exon 6 with the disease associated C allele at rs6897932.
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27
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Danoff JS, Wroblewski KL, Graves AJ, Quinn GC, Perkeybile AM, Kenkel WM, Lillard TS, Parikh HI, Golino HF, Gregory SG, Carter CS, Bales KL, Connelly JJ. Genetic, epigenetic, and environmental factors controlling oxytocin receptor gene expression. Clin Epigenetics 2021; 13:23. [PMID: 33516250 PMCID: PMC7847178 DOI: 10.1186/s13148-021-01017-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The neuropeptide oxytocin regulates mammalian social behavior. Disruptions in oxytocin signaling are a feature of many psychopathologies. One commonly studied biomarker for oxytocin involvement in psychiatric diseases is DNA methylation at the oxytocin receptor gene (OXTR). Such studies focus on DNA methylation in two regions of OXTR, exon 3 and a region termed MT2 which overlaps exon 1 and intron 1. However, the relative contribution of exon 3 and MT2 in regulating OXTR gene expression in the brain is currently unknown. RESULTS Here, we use the prairie vole as a translational animal model to investigate genetic, epigenetic, and environmental factors affecting Oxtr gene expression in a region of the brain that has been shown to drive Oxtr related behavior in the vole, the nucleus accumbens. We show that the genetic structure of Oxtr in prairie voles resembles human OXTR. We then studied the effects of early life experience on DNA methylation in two regions of a CpG island surrounding the Oxtr promoter: MT2 and exon 3. We show that early nurture in the form of parental care results in DNA hypomethylation of Oxtr in both MT2 and exon 3, but only DNA methylation in MT2 is associated with Oxtr gene expression. Network analyses indicate that CpG sites in the 3' portion of MT2 are most highly associated with Oxtr gene expression. We also identify two novel SNPs in exon 3 of Oxtr in prairie voles and a novel alternative transcript originating from the third intron of the gene. Expression of the novel alternative transcript is associated with genotype at SNP KLW2. CONCLUSIONS These results identify putative regulatory features of Oxtr in prairie voles which inform future studies examining OXTR in human social behaviors and disorders. These studies indicate that in prairie voles, DNA methylation in MT2, particularly in the 3' portion, is more predictive of Oxtr gene expression than DNA methylation in exon 3. Similarly, in human temporal cortex, we find that DNA methylation in the 3' portion of MT2 is associated with OXTR expression. Together, these results suggest that among the CpG sites studied, DNA methylation of MT2 may be the most reliable indicator of OXTR gene expression. We also identify novel features of prairie vole Oxtr, including SNPs and an alternative transcript, which further develop the prairie vole as a translational model for studies of OXTR.
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Affiliation(s)
- Joshua S Danoff
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Kelly L Wroblewski
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Andrew J Graves
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Graham C Quinn
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Allison M Perkeybile
- The Kinsey Institute, Indiana University, 150 S Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - William M Kenkel
- The Kinsey Institute, Indiana University, 150 S Woodlawn Avenue, Bloomington, IN, 47405, USA
- Department of Psychological and Brain Sciences, University of Delaware, 105 The Green, Newark, DE, 19716, USA
| | - Travis S Lillard
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Hardik I Parikh
- Division of Infectious Diseases and International Health, University of Virginia, 345 Crispell Drive, Charlottesville, VA, 22908, USA
- Research Computing, University of Virginia, 560 Ray C. Hunt Drive, Charlottesville, VA, 22903, USA
| | - Hudson F Golino
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, 300 N Duke St, Durham, NC, 27701, USA
| | - C Sue Carter
- The Kinsey Institute, Indiana University, 150 S Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Karen L Bales
- Department of Psychology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Jessica J Connelly
- Department of Psychology, University of Virginia, 102 Gilmer Hall, P.O. Box 400400, Charlottesville, VA, 22904, USA.
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28
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SoRelle ED, Dai J, Bonglack EN, Heckenberg EM, Zhou JY, Giamberardino SN, Bailey JA, Gregory SG, Chan C, Luftig MA. Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines. eLife 2021; 10:62586. [PMID: 33501914 PMCID: PMC7867410 DOI: 10.7554/elife.62586] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 08/29/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) are generated by transforming primary B cells with Epstein–Barr virus (EBV) and are used extensively as model systems in viral oncology, immunology, and human genetics research. In this study, we characterized single-cell transcriptomic profiles of five LCLs and present a simple discrete-time simulation to explore the influence of stochasticity on LCL clonal evolution. Single-cell RNA sequencing (scRNA-seq) revealed substantial phenotypic heterogeneity within and across LCLs with respect to immunoglobulin isotype; virus-modulated host pathways involved in survival, activation, and differentiation; viral replication state; and oxidative stress. This heterogeneity is likely attributable to intrinsic variance in primary B cells and host–pathogen dynamics. Stochastic simulations demonstrate that initial primary cell heterogeneity, random sampling, time in culture, and even mild differences in phenotype-specific fitness can contribute substantially to dynamic diversity in populations of nominally clonal cells.
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Affiliation(s)
- Elliott D SoRelle
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, United States
| | - Joanne Dai
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States
| | - Emmanuela N Bonglack
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States.,Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States
| | - Emma M Heckenberg
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States
| | - Jeffrey Y Zhou
- Department of Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Stephanie N Giamberardino
- Duke Molecular Physiology Institute and Department of Neurology, Duke University School of Medicine, Durham, United States
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, United States
| | - Simon G Gregory
- Duke Molecular Physiology Institute and Department of Neurology, Duke University School of Medicine, Durham, United States
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, United States
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, United States
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29
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Spanos M, Chandrasekhar T, Kim SJ, Hamer RM, King BH, McDougle CJ, Sanders KB, Gregory SG, Kolevzon A, Veenstra-VanderWeele J, Sikich L. Rationale, design, and methods of the Autism Centers of Excellence (ACE) network Study of Oxytocin in Autism to improve Reciprocal Social Behaviors (SOARS-B). Contemp Clin Trials 2020; 98:106103. [PMID: 32777383 DOI: 10.1016/j.cct.2020.106103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 12/01/2022]
Abstract
OBJECTIVE To describe the rationale, design, and methods of the Autism Centers of Excellence (ACE) network Study of Oxytocin in Autism to improve Reciprocal Social Behaviors (SOARS-B). METHOD This phase 2 clinical trial was designed to evaluate the use of intranasal oxytocin treatment to improve social difficulties in individuals with autism spectrum disorder (ASD). In total, 290 participants ages 3 to 17 years with a DSM-5 diagnosis of ASD were enrolled to receive 24 weeks of treatment with either oxytocin or a matched placebo at one of seven collaborating sites. Participants were subsequently treated with open-label oxytocin for 24 additional weeks. Post-treatment assessments were done approximately 4 weeks after treatment discontinuation. Plasma oxytocin and oxytocin receptor gene (OXTR) methylation level were measured at baseline, and week 8, 24 and 36 to explore potential relationships between these biomarkers and treatment response. RESULTS This report describes the rationale, design, and methods of the SOARS-B clinical trial. CONCLUSIONS There is a tremendous unmet need for safe and effective pharmacological treatment options that target the core symptoms of ASD. Several studies support the hypothesis that intranasal oxytocin could improve social orienting and the salience of social rewards in ASD, thereby enhancing reciprocal social behaviors. However, due to conflicting results from a number of pilot studies on the prosocial effects of exogenous oxytocin, this hypothesis remains controversial and inconclusive. SOARS-B is the best powered study to date to address this hypothesis and promises to improve our understanding of the safety and efficacy of intranasal oxytocin in the treatment of social deficits in children with ASD.
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Affiliation(s)
- Marina Spanos
- Duke Center for Autism and Brain Development, Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America.
| | - Tara Chandrasekhar
- Duke Center for Autism and Brain Development, Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
| | - Soo-Jeong Kim
- Seattle Children's Autism Center, Department of Psychiatry and Behavioral Sciences, University of Washington; Seattle, WA, United States of America
| | - Robert M Hamer
- Departments of Psychiatry and Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Bryan H King
- Department of Psychiatry and Weill Institute for Neurosciences, University of California San Francisco, UCSF Benioff Children's Hospitals, San Francisco, CA, United States of America
| | - Christopher J McDougle
- Lurie Center for Autism, Massachusetts General Hospital; Department of Psychiatry, Harvard Medical School, Boston, MA, United States of America
| | - Kevin B Sanders
- Neuroscience Product Development, F. Hoffmann-La Roche, Basel, Switzerland
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America; Department of Neurology, Duke University School of Medicine, Durham, NC, United States of America
| | - Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jeremy Veenstra-VanderWeele
- Department of Psychiatry, Columbia University; New York State Psychiatric Institute; Center for Autism and the Developing Brain, New York-Presbyterian Hospital, United States of America
| | - Linmarie Sikich
- Duke Center for Autism and Brain Development, Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
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30
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Baht GS, Bareja A, Lee DE, Rao RR, Huang R, Huebner JL, Bartlett DB, Hart CR, Gibson JR, Lanza IR, Kraus VB, Gregory SG, Spiegelman BM, White JP. Author Correction: Meteorin-like facilitates skeletal muscle repair through a Stat3/IGF-1 mechanism. Nat Metab 2020; 2:794. [PMID: 32694832 DOI: 10.1038/s42255-020-0257-y] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Akshay Bareja
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - David E Lee
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Rajesh R Rao
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Rong Huang
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Janet L Huebner
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - David B Bartlett
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC, USA
| | - Corey R Hart
- Division of Endocrinology and Metabolism, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ian R Lanza
- Division of Endocrinology and Metabolism, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Virginia B Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Bruce M Spiegelman
- Dana-Farber Cancer Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - James P White
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA.
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31
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Becker KC, Kwee LC, Neely ML, Grass E, Jakubowski JA, Fox KAA, White HD, Gregory SG, Gurbel PA, Carvalho LDP, Becker RC, Magnus Ohman E, Roe MT, Shah SH, Chan MY. Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements. Sci Rep 2020; 10:6169. [PMID: 32277149 PMCID: PMC7148370 DOI: 10.1038/s41598-020-63263-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/24/2020] [Indexed: 12/12/2022] Open
Abstract
Changes in platelet physiology are associated with simultaneous changes in microRNA concentrations, suggesting a role for microRNA in platelet regulation. Here we investigated potential associations between microRNA and platelet reactivity (PR), a marker of platelet function, in two cohorts following a non-ST elevation acute coronary syndrome (NSTE-ACS) event. First, non-targeted microRNA concentrations and PR were compared in a case (N = 77) control (N = 76) cohort within the larger TRILOGY-ACS trial. MicroRNA significant in this analysis plus CVD-associated microRNAs from the literature were then quantified by targeted rt-PCR in the complete TRILOGY-ACS cohort (N = 878) and compared with matched PR samples. Finally, microRNA significant in the non-targeted & targeted analyses were verified in an independent post NSTE-ACS cohort (N = 96). From the non-targeted analysis, 14 microRNAs were associated with PR (Fold Change: 0.91–1.27, p-value: 0.004–0.05). From the targeted analysis, five microRNAs were associated with PR (Beta: −0.09–0.22, p-value: 0.004–0.05). Of the 19 significant microRNAs, three, miR-15b-5p, miR-93 and miR-126, were consistently associated with PR in the TRILOGY-ACS and independent Singapore post-ACS cohorts, suggesting the measurement of circulating microRNA concentrations may report on dynamic changes in platelet biology following a cardiovascular ischemic event.
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Affiliation(s)
| | | | | | | | | | | | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital, Auckland, New Zealand
| | | | - Paul A Gurbel
- Inova Heart & Vascular Institute, Falls Church, VA, USA
| | | | | | - E Magnus Ohman
- Duke Clinical Research Institute, Durham, NC, USA.,Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | - Matthew T Roe
- Duke Clinical Research Institute, Durham, NC, USA.,Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | - Svati H Shah
- Duke Molecular Physiology Institute, Durham, NC, USA.,Duke Clinical Research Institute, Durham, NC, USA.,Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | - Mark Y Chan
- National University of Singapore, Singapore, Singapore.
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32
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Baht GS, Bareja A, Lee DE, Rao RR, Huang R, Huebner JL, Bartlett DB, Hart CR, Gibson JR, Lanza IR, Kraus VB, Gregory SG, Spiegelman BM, White JP. Meteorin-like facilitates skeletal muscle repair through a Stat3/IGF-1 mechanism. Nat Metab 2020; 2:278-289. [PMID: 32694780 PMCID: PMC7504545 DOI: 10.1038/s42255-020-0184-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/17/2020] [Indexed: 01/14/2023]
Abstract
The immune system plays a multifunctional role throughout the regenerative process, regulating both pro-/anti-inflammatory phases and progenitor cell function. In the present study, we identify the myokine/cytokine Meteorin-like (Metrnl) as a critical regulator of muscle regeneration. Mice genetically lacking Metrnl have impaired muscle regeneration associated with a reduction in immune cell infiltration and an inability to transition towards an anti-inflammatory phenotype. Isochronic parabiosis, joining wild-type and whole-body Metrnl knock-out (KO) mice, returns Metrnl expression in the injured muscle and improves muscle repair, providing supportive evidence for Metrnl secretion from infiltrating immune cells. Macrophage-specific Metrnl KO mice are also deficient in muscle repair. During muscle regeneration, Metrnl works, in part, through Stat3 activation in macrophages, resulting in differentiation to an anti-inflammatory phenotype. With regard to myogenesis, Metrnl induces macrophage-dependent insulin-like growth factor 1 production, which has a direct effect on primary muscle satellite cell proliferation. Perturbations in this pathway inhibit efficacy of Metrnl in the regenerative process. Together, these studies identify Metrnl as an important regulator of muscle regeneration and a potential therapeutic target to enhance tissue repair.
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Affiliation(s)
- Gurpreet S Baht
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Akshay Bareja
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - David E Lee
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Rajesh R Rao
- Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Rong Huang
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Janet L Huebner
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - David B Bartlett
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC, USA
| | - Corey R Hart
- Division of Endocrinology and Metabolism, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ian R Lanza
- Division of Endocrinology and Metabolism, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Virginia B Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
| | - Bruce M Spiegelman
- Dana-Farber Cancer Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - James P White
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Durham, NC, USA.
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33
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Jewell ML, Gibson JR, Guy CD, Hyun J, Du K, Oh SH, Premont RT, Hsu DS, Ribar T, Gregory SG, Diehl AME. Single-Cell RNA Sequencing Identifies Yes-Associated Protein 1-Dependent Hepatic Mesothelial Progenitors in Fibrolamellar Carcinoma. Am J Pathol 2020; 190:93-107. [PMID: 31669305 PMCID: PMC10069284 DOI: 10.1016/j.ajpath.2019.09.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/23/2019] [Accepted: 09/26/2019] [Indexed: 12/29/2022]
Abstract
Fibrolamellar carcinoma (FLC) is characterized by in-frame fusion of DnaJ heat shock protein family (Hsp40) member B1 (DNAJB1) with protein kinase cAMP-activated catalytic subunit α (PRKACA) and by dense desmoplasia. Surgery is the only effective treatment because mechanisms supporting tumor survival are unknown. We used single-cell RNA sequencing to characterize a patient-derived FLC xenograft model and identify therapeutic targets. Human FLC cells segregated into four discrete clusters that all expressed the oncogene Yes-associated protein 1 (YAP1). The two communities most enriched with cells coexpressing FLC markers [CD68, A-kinase anchoring protein 12 (AKAP12), cytokeratin 7, epithelial cell adhesion molecule (EPCAM), and carbamoyl palmitate synthase-1] also had the most cells expressing YAP1 and its proproliferative target genes (AREG and CCND1), suggesting these were proliferative FLC cell clusters. The other two clusters were enriched with cells expressing profibrotic YAP1 target genes, ACTA2, ELN, and COL1A1, indicating these were fibrogenic FLC cells. All clusters expressed the YAP1 target gene and mesothelial progenitor marker mesothelin, and many mesothelin-positive cells coexpressed albumin. Trajectory analysis predicted that the four FLC communities were derived from a single cell type transitioning among phenotypic states. After establishing a novel FLC cell line that harbored the DNAJB1-PRKACA fusion, YAP1 was inhibited, which significantly reduced expression of known YAP1 target genes as well as cell growth and migration. Thus, both FLC epithelial and stromal cells appear to arise from DNAJB1-PRKACA fusion in a YAP1-dependent liver mesothelial progenitor, identifying YAP1 as a target for FLC therapy.
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Affiliation(s)
- Mark L Jewell
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Cynthia D Guy
- Department of Pathology, Duke University, Durham, North Carolina
| | - Jeongeun Hyun
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Kuo Du
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Seh-Hoon Oh
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Richard T Premont
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - David S Hsu
- Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Thomas Ribar
- Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Anna Mae E Diehl
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina.
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34
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Gupta S, Hovelson DH, Kemeny G, Halabi S, Foo WC, Anand M, Somarelli JA, Tomlins SA, Antonarakis ES, Luo J, Dittamore RV, George DJ, Rothwell C, Nanus DM, Armstrong AJ, Gregory SG. Discordant and heterogeneous clinically relevant genomic alterations in circulating tumor cells vs plasma DNA from men with metastatic castration resistant prostate cancer. Genes Chromosomes Cancer 2019; 59:225-239. [PMID: 31705765 DOI: 10.1002/gcc.22824] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor cell (CTC) and cell-free (cf) DNA-based genomic alterations are increasingly being used for clinical decision-making in oncology. However, the concordance and discordance between paired CTC and cfDNA genomic profiles remain largely unknown. We performed comparative genomic hybridization (CGH) on CTCs and cfDNA, and low-pass whole genome sequencing (lpWGS) on cfDNA to characterize genomic alterations (CNA) and tumor content in two independent prospective studies of 93 men with mCRPC treated with enzalutamide/abiraterone, or radium-223. Comprehensive analysis of 69 patient CTCs and 72 cfDNA samples from 93 men with mCRPC, including 64 paired samples, identified common concordant gains in FOXA1, AR, and MYC, and losses in BRCA1, PTEN, and RB1 between CTCs and cfDNA. Concordant PTEN loss and discordant BRCA2 gain were associated with significantly worse outcomes in Epic AR-V7 negative men with mCRPC treated with abiraterone/enzalutamide. We identified and externally validated CTC-specific genomic alternations that were discordant in paired cfDNA, even in samples with high tumor content. These CTC/cfDNA-discordant regions included key genomic regulators of lineage plasticity, osteomimicry, and cellular differentiation, including MYCN gain in CTCs (31%) that was rarely detected in cfDNA. CTC MYCN gain was associated with poor clinical outcomes in AR-V7 negative men and small cell transformation. In conclusion, we demonstrated concordance of multiple genomic alterations across CTC and cfDNA platforms; however, some genomic alterations displayed substantial discordance between CTC DNA and cfDNA despite the use of identical copy number analysis methods, suggesting tumor heterogeneity and divergent evolution associated with poor clinical outcomes.
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Affiliation(s)
- Santosh Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Daniel H Hovelson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Gabor Kemeny
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Susan Halabi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina
| | - Wen-Chi Foo
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Monika Anand
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Jason A Somarelli
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Department of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan
| | - Emmanuel S Antonarakis
- Prostate Cancer Research Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jun Luo
- James Buchanan Brady Urological Institute and the Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Daniel J George
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - Colin Rothwell
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina
| | - David M Nanus
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Department of Medicine, Surgery, Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Simon G Gregory
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
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Abdulrahim JW, Kwee LC, Grass E, Siegler IC, Williams R, Karra R, Kraus WE, Gregory SG, Shah SH. Epigenome-Wide Association Study for All-Cause Mortality in a Cardiovascular Cohort Identifies Differential Methylation in Castor Zinc Finger 1 ( CASZ1). J Am Heart Assoc 2019; 8:e013228. [PMID: 31642367 PMCID: PMC6898816 DOI: 10.1161/jaha.119.013228] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023]
Abstract
Background DNA methylation is implicated in many chronic diseases and may contribute to mortality. Therefore, we conducted an epigenome-wide association study (EWAS) for all-cause mortality with whole-transcriptome data in a cardiovascular cohort (CATHGEN [Catheterization Genetics]). Methods and Results Cases were participants with mortality≥7 days postcatheterization whereas controls were alive with≥2 years of follow-up. The Illumina Human Methylation 450K and EPIC arrays (Illumina, San Diego, CA) were used for the discovery and validation sets, respectively. A linear model approach with empirical Bayes estimators adjusted for confounders was used to assess difference in methylation (Δβ). In the discovery set (55 cases, 49 controls), 25 629 (6.5%) probes were differently methylated (P<0.05). In the validation set (108 cases, 108 controls), 3 probes were differentially methylated with a false discovery rate-adjusted P<0.10: cg08215811 (SLC4A9; log2 fold change=-0.14); cg17845532 (MATK; fold change=-0.26); and cg17944110 (castor zinc finger 1 [CASZ1]; FC=0.26; P<0.0001; false discovery rate-adjusted P=0.046-0.080). Meta-analysis identified 6 probes (false discovery rate-adjusted P<0.05): the 3 above, cg20428720 (intergenic), cg17647904 (NCOR2), and cg23198793 (CAPN3). Messenger RNA expression of 2 MATK isoforms was lower in cases (fold change=-0.24 [P=0.007] and fold change=-0.61 [P=0.009]). The CASZ1, NCOR2, and CAPN3 transcripts did not show differential expression (P>0.05); the SLC4A9 transcript did not pass quality control. The cg17944110 probe is located within a potential regulatory element; expression of predicted targets (using GeneHancer) of the regulatory element, UBIAD1 (P=0.01) and CLSTN1 (P=0.03), were lower in cases. Conclusions We identified 6 novel methylation sites associated with all-cause mortality. Methylation in CASZ1 may serve as a regulatory element associated with mortality in cardiovascular patients. Larger studies are necessary to confirm these observations.
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Affiliation(s)
- Jawan W. Abdulrahim
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Lydia Coulter Kwee
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Elizabeth Grass
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Ilene C. Siegler
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNC
| | - Redford Williams
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNC
| | - Ravi Karra
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
| | - William E. Kraus
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
| | - Simon G. Gregory
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Svati H. Shah
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
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36
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Kwee LC, Neely ML, Grass E, Gregory SG, Roe MT, Ohman EM, Fox KAA, White HD, Armstrong PW, Bowsman LM, Haas JV, Duffin KL, Chan MY, Shah SH. Associations of osteopontin and NT-proBNP with circulating miRNA levels in acute coronary syndrome. Physiol Genomics 2019; 51:506-515. [PMID: 31530226 PMCID: PMC7054637 DOI: 10.1152/physiolgenomics.00033.2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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] [Indexed: 12/11/2022] Open
Abstract
The genomic regulatory networks underlying the pathogenesis of non-ST-segment elevation acute coronary syndrome (NSTE-ACS) are incompletely understood. As intermediate traits, protein biomarkers report on underlying disease severity and prognosis in NSTE-ACS. We hypothesized that integration of dense microRNA (miRNA) profiling with biomarker measurements would highlight potential regulatory pathways that underlie the relationships between prognostic biomarkers, miRNAs, and cardiovascular phenotypes. We performed miRNA sequencing using whole blood from 186 patients from the TRILOGY-ACS trial. Seven circulating prognostic biomarkers were measured: NH2-terminal pro-B-type natriuretic peptide (NT-proBNP), high-sensitivity C-reactive protein, osteopontin (OPN), myeloperoxidase, growth differentiation factor 15, monocyte chemoattractant protein, and neopterin. We tested miRNAs for association with each biomarker with generalized linear models and controlled the false discovery rate at 0.05. Ten miRNAs, including known cardiac-related miRNAs 25-3p and 423-3p, were associated with NT-proBNP levels (min. P = 7.5 × 10−4) and 48 miRNAs, including cardiac-related miRNAs 378a-3p, 20b-5p and 320a, -b, and -d, were associated with OPN levels (min. P = 1.6 × 10−6). NT-proBNP and OPN were also associated with time to cardiovascular death, myocardial infarction (MI), or stroke in the sample. By integrating large-scale miRNA profiling with circulating biomarkers as intermediate traits, we identified associations of known cardiac-related and novel miRNAs with two prognostic biomarkers and identified potential genomic networks regulating these biomarkers. These results, highlighting plausible biological pathways connecting miRNAs with biomarkers and outcomes, may inform future studies seeking to delineate genomic pathways underlying NSTE-ACS outcomes.
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Affiliation(s)
| | - Megan L Neely
- Duke Clinical Research Institute, Durham, North Carolina
| | | | - Simon G Gregory
- Duke Molecular Physiology Institute, Durham, North Carolina.,Department of Neurology, Duke University School of Medicine, Durham, North Carolina
| | - Matthew T Roe
- Duke Clinical Research Institute, Durham, North Carolina.,Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - E Magnus Ohman
- Duke Clinical Research Institute, Durham, North Carolina.,Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Keith A A Fox
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital, Auckland, New Zealand
| | - Paul W Armstrong
- Canadian VIGOUR Centre and Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Lenden M Bowsman
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Joseph V Haas
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Kevin L Duffin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Mark Y Chan
- Division of Cardiology, Department of Medicine, National University of Singapore, Singapore
| | - Svati H Shah
- Duke Molecular Physiology Institute, Durham, North Carolina.,Duke Clinical Research Institute, Durham, North Carolina.,Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
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Armstrong AJ, Gupta S, Healy P, Kemeny G, Leith B, Zalutsky MR, Spritzer C, Davies C, Rothwell C, Ware K, Somarelli JA, Wood K, Ribar T, Giannakakou P, Zhang J, Gerber D, Anand M, Foo WC, Halabi S, Gregory SG, George DJ. Pharmacodynamic study of radium-223 in men with bone metastatic castration resistant prostate cancer. PLoS One 2019; 14:e0216934. [PMID: 31136607 PMCID: PMC6538141 DOI: 10.1371/journal.pone.0216934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 10/24/2018] [Accepted: 04/28/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Radium-223 is a targeted alpha-particle therapy that improves survival in men with metastatic castration resistant prostate cancer (mCRPC), particularly in men with elevated serum levels of bone alkaline phosphatase (B-ALP). We hypothesized that osteomimicry, a form of epithelial plasticity leading to an osteoblastic phenotype, may contribute to intralesional deposition of radium-223 and subsequent irradiation of the tumor microenvironment. METHODS We conducted a pharmacodynamic study (NCT02204943) of radium-223 in men with bone mCRPC. Prior to and three and six months after radium-223 treatment initiation, we collected CTCs and metastatic biopsies for phenotypic characterization and CTC genomic analysis. The primary objective was to describe the impact of radium-223 on the prevalence of CTC B-ALP over time. We measured radium-223 decay products in tumor and surrounding normal bone during treatment. We validated genomic findings in a separate independent study of men with bone metastatic mCRPC (n = 45) and publicly accessible data of metastatic CRPC tissues. RESULTS We enrolled 20 men with symptomatic bone predominant mCRPC and treated with radium-223. We observed greater radium-223 radioactivity levels in metastatic bone tumor containing biopsies compared with adjacent normal bone. We found evidence of persistent Cellsearch CTCs and B-ALP (+) CTCs in the majority of men over time during radium-223 therapy despite serum B-ALP normalization. We identified genomic gains in osteoblast mimicry genes including gains of ALPL, osteopontin, SPARC, OB-cadherin and loss of RUNX2, and validated genomic alterations or increased expression at the DNA and RNA level in an independent cohort of 45 men with bone-metastatic CRPC and in 150 metastatic biopsies from men with mCRPC. CONCLUSIONS Osteomimicry may contribute in part to the uptake of radium-223 within bone metastases and may thereby enhance the therapeutic benefit of this bone targeting radiotherapy.
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Affiliation(s)
- Andrew J. Armstrong
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
- * E-mail:
| | - Santosh Gupta
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University, Durham, NC, United States of America
| | - Patrick Healy
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
- Department of Biostatistics, Duke University, Durham, NC, United States of America
| | - Gabor Kemeny
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
| | - Beth Leith
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
| | - Michael R. Zalutsky
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
- Department of Radiology, Duke University, Durham, NC, United States of America
| | - Charles Spritzer
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
- Department of Radiology, Duke University, Durham, NC, United States of America
| | - Catrin Davies
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
| | - Colin Rothwell
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
| | - Kathryn Ware
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
| | - Jason A. Somarelli
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
| | - Kris Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, United States of America
| | - Thomas Ribar
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, United States of America
| | | | - Jiaren Zhang
- Weill Cornell Medical College, New York, NY, United States of America
| | - Drew Gerber
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
| | - Monika Anand
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
| | - Wen-Chi Foo
- Duke Department of Pathology, Duke University, Durham, NC, United States of America
| | - Susan Halabi
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
- Department of Biostatistics, Duke University, Durham, NC, United States of America
| | - Simon G. Gregory
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University, Durham, NC, United States of America
| | - Daniel J. George
- Department of Medicine, Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC, United States of America
- Duke Prostate and Urologic Cancer Center, Duke Cancer Institute, Durham, NC, United States of America
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Tailor TD, Rao X, Campa MJ, Wang J, Gregory SG, Patz EF. Whole Exome Sequencing of Cell-Free DNA for Early Lung Cancer: A Pilot Study to Differentiate Benign From Malignant CT-Detected Pulmonary Lesions. Front Oncol 2019; 9:317. [PMID: 31069172 PMCID: PMC6491780 DOI: 10.3389/fonc.2019.00317] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 01/15/2019] [Accepted: 04/08/2019] [Indexed: 12/18/2022] Open
Abstract
Introduction: Indeterminate pulmonary lesions (IPL) detected by CT pose a significant clinical challenge, frequently necessitating long-term surveillance or biopsy for diagnosis. In this pilot investigation, we performed whole exome sequencing (WES) of plasma cell free (cfDNA) and matched germline DNA in patients with CT-detected pulmonary lesions to determine the feasibility of somatic cfDNA mutations to differentiate benign from malignant pulmonary nodules. Methods: 33 patients with a CT-detected pulmonary lesions were retrospectively enrolled (n = 16 with a benign nodule, n = 17 with a malignant nodule). Following isolation and amplification of plasma cfDNA and matched peripheral blood mononuclear cells (PBMC) from patient blood samples, WES of cfDNA and PBMC DNA was performed. After genomic alignment and filtering, we looked for lung-cancer associated driver mutations and next identified high-confidence somatic variants in both groups. Results: Somatic cfDNA mutations were observed in both groups, with the cancer group demonstrating more variants than the benign group (1083 ± 476 versus 553 ± 519, p < 0.0046). By selecting variants present in >2 cancer patients and not the benign group, we accurately identified 82% (14/17) of cancer patients. Conclusions: This study suggests a potential role for cfDNA for the early identification of lung cancer in patients with CT-detected pulmonary lesions. Importantly, a substantial number of somatic variants in healthy patients with benign pulmonary nodules were also found. Such "benign" variants, while largely unexplored to date, have widespread relevance to all liquid biopsies if cfDNA is to be used accurately for cancer detection.
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Affiliation(s)
- Tina D Tailor
- Department of Radiology, Duke University Medical Center, Durham, NC, United States
| | - Xiayu Rao
- Division of Quantitative Sciences, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Michael J Campa
- Department of Radiology, Duke University Medical Center, Durham, NC, United States
| | - Jing Wang
- Division of Quantitative Sciences, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States
| | - Edward F Patz
- Department of Radiology, Duke University Medical Center, Durham, NC, United States.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States
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Armstrong AJ, Halabi S, Luo J, Nanus DM, Giannakakou P, Szmulewitz RZ, Danila DC, Healy P, Anand M, Rothwell CJ, Rasmussen J, Thornburg B, Berry WR, Wilder RS, Lu C, Chen Y, Silberstein JL, Kemeny G, Galletti G, Somarelli JA, Gupta S, Gregory SG, Scher HI, Dittamore R, Tagawa ST, Antonarakis ES, George DJ. Prospective Multicenter Validation of Androgen Receptor Splice Variant 7 and Hormone Therapy Resistance in High-Risk Castration-Resistant Prostate Cancer: The PROPHECY Study. J Clin Oncol 2019; 37:1120-1129. [PMID: 30865549 PMCID: PMC6494355 DOI: 10.1200/jco.18.01731] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Androgen receptor splice variant 7 (AR-V7) results in a truncated receptor, which leads to ligand-independent constitutive activation that is not inhibited by anti-androgen therapies, including abiraterone or enzalutamide. Given that previous reports suggested that circulating tumor cell (CTC) AR-V7 detection is a poor prognostic indicator for the clinical efficacy of secondary hormone therapies, we conducted a prospective multicenter validation study. PATIENTS AND METHODS PROPHECY (ClinicalTrials.gov identifier: NCT02269982) is a multicenter, prospective-blinded study of men with high-risk mCRPC starting abiraterone acetate or enzalutamide treatment. The primary objective was to validate the prognostic significance of baseline CTC AR-V7 on the basis of radiographic or clinical progression free-survival (PFS) by using the Johns Hopkins University modified-AdnaTest CTC AR-V7 mRNA assay and the Epic Sciences CTC nuclear-specific AR-V7 protein assay. Overall survival (OS) and prostate-specific antigen responses were secondary end points. RESULTS We enrolled 118 men with mCRPC who were starting abiraterone or enzalutamide treatment. AR-V7 detection by both the Johns Hopkins and Epic AR-V7 assays was independently associated with shorter PFS (hazard ratio, 1.9 [95% CI, 1.1 to 3.3; P = .032] and 2.4 [95% CI, 1.1 to 5.1; P = .020], respectively) and OS (hazard ratio, 4.2 [95% CI, 2.1 to 8.5] and 3.5 [95% CI, 1.6 to 8.1], respectively) after adjusting for CTC number and clinical prognostic factors. Men with AR-V7–positive mCRPC had fewer confirmed prostate-specific antigen responses (0% to 11%) or soft tissue responses (0% to 6%). The observed percentage agreement between the two AR-V7 assays was 82%. CONCLUSION Detection of AR-V7 in CTCs by two blood-based assays is independently associated with shorter PFS and OS with abiraterone or enzalutamide, and such men with mCRPC should be offered alternative treatments.
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Affiliation(s)
| | | | - Jun Luo
- 2 Johns Hopkins University, Baltimore, MD
| | | | | | | | - Daniel C Danila
- 3 Weill Cornell Medical College, New York, NY.,5 Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | - Yan Chen
- 2 Johns Hopkins University, Baltimore, MD
| | | | | | | | | | | | | | - Howard I Scher
- 3 Weill Cornell Medical College, New York, NY.,5 Memorial Sloan Kettering Cancer Center, New York, NY
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40
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Perkeybile AM, Carter CS, Wroblewski KL, Puglia MH, Kenkel WM, Lillard TS, Karaoli T, Gregory SG, Mohammadi N, Epstein L, Bales KL, Connelly JJ. Early nurture epigenetically tunes the oxytocin receptor. Psychoneuroendocrinology 2019; 99:128-136. [PMID: 30227351 PMCID: PMC6231974 DOI: 10.1016/j.psyneuen.2018.08.037] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/21/2022]
Abstract
Mammalian sociality is regulated in part by the neuropeptide oxytocin. In prairie voles, subtle variation in early life experience changes oxytocin receptor-mediated social behaviors. We report that low levels of early care in voles leads to de novo DNA methylation at specific regulatory sites in the oxytocin receptor gene (Oxtr), impacting gene expression and protein distribution in the nucleus accumbens. DNA methylation state of the blood predicts expression in the brain indicating the utility of the blood as a biomarker for the transcription state of the brain. These experience-sensitive CpG sites are conserved in humans, are related to gene expression in the brain, and have been associated with psychiatric disorders and individual differences in neural response to social stimuli. These results identify a mechanism by which early care regulates later displays of typical prairie vole social behavior and suggest the potential for nurture driven epigenetic tuning of OXTR in humans.
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Affiliation(s)
- Allison M. Perkeybile
- Indiana University, The Kinsey Institute, 1165 E 3rd St, Morrison Hall 313, Bloomington, IN, 47405
| | - C. Sue Carter
- Indiana University, The Kinsey Institute, 1165 E 3rd St, Morrison Hall 313, Bloomington, IN, 47405
| | - Kelly L. Wroblewski
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - Meghan H. Puglia
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - William M. Kenkel
- Indiana University, The Kinsey Institute, 1165 E 3rd St, Morrison Hall 313, Bloomington, IN, 47405
| | - Travis S. Lillard
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - Themistoclis Karaoli
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
| | - Simon G. Gregory
- Duke University, Duke Molecular Physiology Institute, 300 N Duke St, Durham, NC, 27701
| | - Niaz Mohammadi
- University of California, Davis, Department of Psychology, One Shields Ave, Davis, CA, 95616
| | - Larissa Epstein
- University of California, Davis, Department of Psychology, One Shields Ave, Davis, CA, 95616
| | - Karen L. Bales
- University of California, Davis, Department of Psychology, One Shields Ave, Davis, CA, 95616
| | - Jessica J. Connelly
- University of Virginia, Department of Psychology, 102 Gilmer Hall, P.O. Box 400400, Charlottesville VA, 22904
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Ward-Caviness CK, Kraus WE, Blach C, Haynes CS, Dowdy E, Miranda ML, Devlin R, Diaz-Sanchez D, Cascio WE, Mukerjee S, Stallings C, Smith LA, Gregory SG, Shah SH, Neas LM, Hauser ER. Associations Between Residential Proximity to Traffic and Vascular Disease in a Cardiac Catheterization Cohort. Arterioscler Thromb Vasc Biol 2017; 38:275-282. [PMID: 29191927 DOI: 10.1161/atvbaha.117.310003] [Citation(s) in RCA: 14] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/10/2017] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Exposure to mobile source emissions is nearly ubiquitous in developed nations and is associated with multiple adverse health outcomes. There is an ongoing need to understand the specificity of traffic exposure associations with vascular outcomes, particularly in individuals with cardiovascular disease. APPROACH AND RESULTS We performed a cross-sectional study using 2124 individuals residing in North Carolina, United States, who received a cardiac catheterization at the Duke University Medical Center. Traffic-related exposure was assessed via 2 metrics: (1) the distance between the primary residence and the nearest major roadway; and (2) location of the primary residence in regions defined based on local traffic patterns. We examined 4 cardiovascular disease outcomes: hypertension, peripheral arterial disease, the number of diseased coronary vessels, and recent myocardial infarction. Statistical models were adjusted for race, sex, smoking, type 2 diabetes mellitus, body mass index, hyperlipidemia, and home value. Results are expressed in terms of the odds ratio (OR). A 23% decrease in residential distance to major roadways was associated with higher prevalence of peripheral arterial disease (OR=1.29; 95% confidence interval, 1.08-1.55) and hypertension (OR=1.15; 95% confidence interval, 1.01-1.31). Associations with peripheral arterial disease were strongest in men (OR=1.42; 95% confidence interval, 1.17-1.74) while associations with hypertension were strongest in women (OR=1.21; 95% confidence interval, 0.99-1.49). Neither myocardial infarction nor the number of diseased coronary vessels were associated with traffic exposure. CONCLUSIONS Traffic-related exposure is associated with peripheral arterial disease and hypertension while no associations are observed for 2 coronary-specific vascular outcomes.
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Affiliation(s)
- Cavin K Ward-Caviness
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.).
| | - William E Kraus
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Colette Blach
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Carol S Haynes
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Elaine Dowdy
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Marie Lynn Miranda
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Robert Devlin
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - David Diaz-Sanchez
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Wayne E Cascio
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Shaibal Mukerjee
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Casson Stallings
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Luther A Smith
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Simon G Gregory
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Svati H Shah
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Lucas M Neas
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
| | - Elizabeth R Hauser
- From the National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC (C.K.W.-C., R.D., D.D.-S., W.E.C., L.M.N.); Duke Molecular Physiology Institute, Durham, NC (W.E.K., C.B., C.S.H., E.D., S.G.G., S.H.S., E.R.H.); Division of Cardiology, Duke University School of Medicine, Durham, NC (W.E.K., S.H.S.); Department of Statistics, Rice University, Houston, TX (M.L.M.); National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC (S.M.); Metabolon, Research Triangle Park, NC (C.S.); Alion Science and Technology, Inc., Research Triangle Park, NC (L.A.S.); and Epidemiologic Research and Information Center, Durham Veterans, Affairs Medical Center, NC (E.R.H.)
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Galarza-Muñoz G, Briggs FBS, Evsyukova I, Schott-Lerner G, Kennedy EM, Nyanhete T, Wang L, Bergamaschi L, Widen SG, Tomaras GD, Ko DC, Bradrick SS, Barcellos LF, Gregory SG, Garcia-Blanco MA. Human Epistatic Interaction Controls IL7R Splicing and Increases Multiple Sclerosis Risk. Cell 2017; 169:72-84.e13. [PMID: 28340352 DOI: 10.1016/j.cell.2017.03.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/18/2016] [Accepted: 03/02/2017] [Indexed: 12/18/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune disorder where T cells attack neurons in the central nervous system (CNS) leading to demyelination and neurological deficits. A driver of increased MS risk is the soluble form of the interleukin-7 receptor alpha chain gene (sIL7R) produced by alternative splicing of IL7R exon 6. Here, we identified the RNA helicase DDX39B as a potent activator of this exon and consequently a repressor of sIL7R, and we found strong genetic association of DDX39B with MS risk. Indeed, we showed that a genetic variant in the 5' UTR of DDX39B reduces translation of DDX39B mRNAs and increases MS risk. Importantly, this DDX39B variant showed strong genetic and functional epistasis with allelic variants in IL7R exon 6. This study establishes the occurrence of biological epistasis in humans and provides mechanistic insight into the regulation of IL7R exon 6 splicing and its impact on MS risk.
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Affiliation(s)
- Gaddiel Galarza-Muñoz
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Center for RNA Biology, Duke University, Durham, NC 27710, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Farren B S Briggs
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Irina Evsyukova
- Center for RNA Biology, Duke University, Durham, NC 27710, USA
| | - Geraldine Schott-Lerner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Edward M Kennedy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Tinashe Nyanhete
- Department of Immunology, Duke University Durham, NC 27710, USA; Department of Surgery, Duke University Durham, NC 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura Bergamaschi
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Georgia D Tomaras
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Durham, NC 27710, USA; Department of Surgery, Duke University Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center; Durham, NC 27710, USA
| | - Shelton S Bradrick
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Center for RNA Biology, Duke University, Durham, NC 27710, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Lisa F Barcellos
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA; Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Mariano A Garcia-Blanco
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Center for RNA Biology, Duke University, Durham, NC 27710, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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43
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Afshari NA, Igo RP, Morris NJ, Stambolian D, Sharma S, Pulagam VL, Dunn S, Stamler JF, Truitt BJ, Rimmler J, Kuot A, Croasdale CR, Qin X, Burdon KP, Riazuddin SA, Mills R, Klebe S, Minear MA, Zhao J, Balajonda E, Rosenwasser GO, Baratz KH, Mootha VV, Patel SV, Gregory SG, Bailey-Wilson JE, Price MO, Price FW, Craig JE, Fingert JH, Gottsch JD, Aldave AJ, Klintworth GK, Lass JH, Li YJ, Iyengar SK. Genome-wide association study identifies three novel loci in Fuchs endothelial corneal dystrophy. Nat Commun 2017; 8:14898. [PMID: 28358029 PMCID: PMC5379100 DOI: 10.1038/ncomms14898] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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: 07/05/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
The structure of the cornea is vital to its transparency, and dystrophies that disrupt corneal organization are highly heritable. To understand the genetic aetiology of Fuchs endothelial corneal dystrophy (FECD), the most prevalent corneal disorder requiring transplantation, we conducted a genome-wide association study (GWAS) on 1,404 FECD cases and 2,564 controls of European ancestry, followed by replication and meta-analysis, for a total of 2,075 cases and 3,342 controls. We identify three novel loci meeting genome-wide significance (P<5 × 10-8): KANK4 rs79742895, LAMC1 rs3768617 and LINC00970/ATP1B1 rs1200114. We also observe an overwhelming effect of the established TCF4 locus. Interestingly, we detect differential sex-specific association at LAMC1, with greater risk in women, and TCF4, with greater risk in men. Combining GWAS results with biological evidence we expand the knowledge of common FECD loci from one to four, and provide a deeper understanding of the underlying pathogenic basis of FECD.
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Affiliation(s)
- Natalie A. Afshari
- Shiley Eye Institute, University of California, La Jolla, California 92093, USA
| | - Robert P. Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Nathan J. Morris
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - V. Lakshmi Pulagam
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Steven Dunn
- Michigan Cornea Consultants, PC, Southfield, Michigan 48034, USA
| | - John F. Stamler
- Department of Ophthalmology, University of Iowa, College of Medicine, Iowa City, Iowa 52242, USA
| | - Barbara J. Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Jacqueline Rimmler
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Abraham Kuot
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | | | - Xuejun Qin
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Kathryn P. Burdon
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Richard Mills
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - Sonja Klebe
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
- Department of Pathology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - Mollie A. Minear
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Jiagang Zhao
- Shiley Eye Institute, University of California, La Jolla, California 92093, USA
| | - Elmer Balajonda
- Duke University Eye Center, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | - Keith H Baratz
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - V. Vinod Mootha
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Sanjay V. Patel
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health and Johns Hopkins University, Baltimore, Maryland 21224, USA
| | | | | | - Jamie E. Craig
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - John H. Fingert
- Department of Ophthalmology, University of Iowa, College of Medicine, Iowa City, Iowa 52242, USA
| | - John D. Gottsch
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Anthony J. Aldave
- Stein Eye Institute, University of California, Los Angeles, California 90095, USA
| | - Gordon K. Klintworth
- Duke University Eye Center, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jonathan H. Lass
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio 44106, USA
| | - Yi-Ju Li
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sudha K. Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio 44106, USA
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Ward-Caviness CK, Neas LM, Blach C, Haynes CS, LaRocque-Abramson K, Grass E, Dowdy ZE, Devlin RB, Diaz-Sanchez D, Cascio WE, Miranda ML, Gregory SG, Shah SH, Kraus WE, Hauser ER. A genome-wide trans-ethnic interaction study links the PIGR-FCAMR locus to coronary atherosclerosis via interactions between genetic variants and residential exposure to traffic. PLoS One 2017; 12:e0173880. [PMID: 28355232 PMCID: PMC5371323 DOI: 10.1371/journal.pone.0173880] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 02/28/2017] [Indexed: 12/31/2022] Open
Abstract
Air pollution is a worldwide contributor to cardiovascular disease mortality and morbidity. Traffic-related air pollution is a widespread environmental exposure and is associated with multiple cardiovascular outcomes such as coronary atherosclerosis, peripheral arterial disease, and myocardial infarction. Despite the recognition of the importance of both genetic and environmental exposures to the pathogenesis of cardiovascular disease, studies of how these two contributors operate jointly are rare. We performed a genome-wide interaction study (GWIS) to examine gene-traffic exposure interactions associated with coronary atherosclerosis. Using race-stratified cohorts of 538 African-Americans (AA) and 1562 European-Americans (EA) from a cardiac catheterization cohort (CATHGEN), we identify gene-by-traffic exposure interactions associated with the number of significantly diseased coronary vessels as a measure of chronic atherosclerosis. We found five suggestive (P<1x10-5) interactions in the AA GWIS, of which two (rs1856746 and rs2791713) replicated in the EA cohort (P < 0.05). Both SNPs are in the PIGR-FCAMR locus and are eQTLs in lymphocytes. The protein products of both PIGR and FCAMR are implicated in inflammatory processes. In the EA GWIS, there were three suggestive interactions; none of these replicated in the AA GWIS. All three were intergenic; the most significant interaction was in a regulatory region associated with SAMSN1, a gene previously associated with atherosclerosis and B cell activation. In conclusion, we have uncovered several novel genes associated with coronary atherosclerosis in individuals chronically exposed to increased ambient concentrations of traffic air pollution. These genes point towards inflammatory pathways that may modify the effects of air pollution on cardiovascular disease risk.
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Affiliation(s)
- Cavin K. Ward-Caviness
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Lucas M. Neas
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Carol S. Haynes
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Karen LaRocque-Abramson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Elizabeth Grass
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Z. Elaine Dowdy
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Robert B. Devlin
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - David Diaz-Sanchez
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Wayne E. Cascio
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Marie Lynn Miranda
- National Center for Geospatial Medicine, Rice University, Houston, TX, United States of America
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Svati H. Shah
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Division of Cardiology, Duke University School of Medicine, Durham, NC, United States of America
| | - William E. Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Division of Cardiology, Duke University School of Medicine, Durham, NC, United States of America
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States of America
- Cooperative Studies Program Epidemiology Center-Durham, Veterans Affairs Medical Center, Durham, NC, United States of America
- * E-mail:
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45
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Sullivan LL, Maloney KA, Towers AJ, Gregory SG, Sullivan BA. Human centromere repositioning within euchromatin after partial chromosome deletion. Chromosome Res 2016; 24:451-466. [PMID: 27581771 DOI: 10.1007/s10577-016-9536-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 07/27/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Centromeres are defined by a specialized chromatin organization that includes nucleosomes that contain the centromeric histone variant centromere protein A (CENP-A) instead of canonical histone H3. Studies in various organisms have shown that centromeric chromatin (i.e., CENP-A chromatin or centrochromatin) exhibits plasticity, in that it can assemble on different types of DNA sequences. However, once established on a chromosome, the centromere is maintained at the same position. In humans, this location is the highly homogeneous repetitive DNA alpha satellite. Mislocalization of centromeric chromatin to atypical locations can lead to genome instability, indicating that restriction of centromeres to a distinct genomic position is important for cell and organism viability. Here, we describe a rearrangement of Homo sapiens chromosome 17 (HSA17) that has placed alpha satellite DNA next to euchromatin. We show that on this mutant chromosome, CENP-A chromatin has spread from the alpha satellite into the short arm of HSA17, establishing a ∼700 kb hybrid centromeric domain that spans both repetitive and unique sequences and changes the expression of at least one gene over which it spreads. Our results illustrate the plasticity of human centromeric chromatin and suggest that heterochromatin normally constrains CENP-A chromatin onto alpha satellite DNA. This work highlights that chromosome rearrangements, particularly those that remove the pericentromere, create opportunities for centromeric nucleosomes to move into non-traditional genomic locations, potentially changing the surrounding chromatin environment and altering gene expression.
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Affiliation(s)
- Lori L Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA
| | - Kristin A Maloney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Aaron J Towers
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, 27710, USA.,Quintiles, 4820 Emperor Blvd., Durham, NC, 27703, USA
| | - Simon G Gregory
- Department of Medicine, Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC, 27701, USA.,Division of Human Genetics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA. .,Quintiles, 4820 Emperor Blvd., Durham, NC, 27703, USA.
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Dungan JR, Qin X, Horne BD, Carlquist JF, Singh A, Hurdle M, Grass E, Haynes C, Gregory SG, Shah SH, Hauser ER, Kraus WE. Case-Only Survival Analysis Reveals Unique Effects of Genotype, Sex, and Coronary Disease Severity on Survivorship. PLoS One 2016; 11:e0154856. [PMID: 27187494 PMCID: PMC4871369 DOI: 10.1371/journal.pone.0154856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/20/2016] [Indexed: 01/05/2023] Open
Abstract
Survival bias may unduly impact genetic association with complex diseases; gene-specific survival effects may further complicate such investigations. Coronary artery disease (CAD) is a complex phenotype for which little is understood about gene-specific survival effects; yet, such information can offer insight into refining genetic associations, improving replications, and can provide candidate genes for both mortality risk and improved survivorship in CAD. Building on our previous work, the purpose of this current study was to: evaluate LSAMP SNP-specific hazards for all-cause mortality post-catheterization in a larger cohort of our CAD cases; and, perform additional replication in an independent dataset. We examined two LSAMP SNPs—rs1462845 and rs6788787—using CAD case-only Cox proportional hazards regression for additive genetic effects, censored on time-to-all-cause mortality or last follow-up among Caucasian subjects from the Catheterization Genetics Study (CATHGEN; n = 2,224) and the Intermountain Heart Collaborative Study (IMHC; n = 3,008). Only after controlling for age, sex, body mass index, histories of smoking, type 2 diabetes, hyperlipidemia and hypertension (HR = 1.11, 95%CI = 1.01–1.22, p = 0.032), rs1462845 conferred significantly increased hazards of all-cause mortality among CAD cases. Even after controlling for multiple covariates, but in only the primary cohort, rs6788787 conferred significantly improved survival (HR = 0.80, 95% CI = 0.69–0.92, p = 0.002). Post-hoc analyses further stratifying by sex and disease severity revealed replicated effects for rs1462845: even after adjusting for aforementioned covariates and coronary interventional procedures, males with severe burden of CAD had significantly amplified hazards of death with the minor variant of rs1462845 in both cohorts (HR = 1.29, 95% CI = 1.08–1.55, p = 0.00456; replication HR = 1.25, 95% CI = 1.05–1.49, p = 0.013). Kaplan-Meier curves revealed unique cohort-specific genotype effects on survival. Additional analyses demonstrated that the homozygous risk genotype (‘A/A’) fully explained the increased hazard in both cohorts. None of the post-hoc analyses in control subjects were significant for any model. This suggests that genetic effects of rs1462845 on survival are unique to CAD presence. This represents formal, replicated evidence of genetic contribution of rs1462845 to increased risk for all-cause mortality; the contribution is unique to CAD case status and specific to males with severe burden of CAD.
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Affiliation(s)
- Jennifer R. Dungan
- Duke University School of Nursing, Durham, NC, United States of America
- * E-mail:
| | - Xuejun Qin
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Benjamin D. Horne
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, United States of America
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States of America
| | - John F. Carlquist
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, United States of America
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States of America
| | - Abanish Singh
- Behavioral Medicine Research Center, Duke University Medical Center, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Melissa Hurdle
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Elizabeth Grass
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Carol Haynes
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Simon G. Gregory
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Svati H. Shah
- Duke University Department of Medicine, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States of America
| | - William E. Kraus
- Duke University Department of Medicine, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
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47
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Zeng Y, Chen H, Ni T, Ruan R, Nie C, Liu X, Feng L, Zhang F, Lu J, Li J, Li Y, Tao W, Gregory SG, Gottschalk W, Lutz MW, Land KC, Yashin A, Tan Q, Yang Z, Bolund L, Ming Q, Yang H, Min J, Willcox DC, Willcox BJ, Gu J, Hauser E, Tian XL, Vaupel JW. Interaction Between the FOXO1A-209 Genotype and Tea Drinking Is Significantly Associated with Reduced Mortality at Advanced Ages. Rejuvenation Res 2016; 19:195-203. [PMID: 26414954 DOI: 10.1089/rej.2015.1737] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
On the basis of the genotypic/phenotypic data from Chinese Longitudinal Healthy Longevity Survey (CLHLS) and Cox proportional hazard model, the present study demonstrates that interactions between carrying FOXO1A-209 genotypes and tea drinking are significantly associated with lower risk of mortality at advanced ages. Such a significant association is replicated in two independent Han Chinese CLHLS cohorts (p = 0.028-0.048 in the discovery and replication cohorts, and p = 0.003-0.016 in the combined dataset). We found the associations between tea drinking and reduced mortality are much stronger among carriers of the FOXO1A-209 genotype compared to non-carriers, and drinking tea is associated with a reversal of the negative effects of carrying FOXO1A-209 minor alleles, that is, from a substantially increased mortality risk to substantially reduced mortality risk at advanced ages. The impacts are considerably stronger among those who carry two copies of the FOXO1A minor allele than those who carry one copy. On the basis of previously reported experiments on human cell models concerning FOXO1A-by-tea-compounds interactions, we speculate that results in the present study indicate that tea drinking may inhibit FOXO1A-209 gene expression and its biological functions, which reduces the negative impacts of FOXO1A-209 gene on longevity (as reported in the literature) and offers protection against mortality risk at oldest-old ages. Our empirical findings imply that the health outcomes of particular nutritional interventions, including tea drinking, may, in part, depend upon individual genetic profiles, and the research on the effects of nutrigenomics interactions could potentially be useful for rejuvenation therapies in the clinic or associated healthy aging intervention programs.
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Affiliation(s)
- Yi Zeng
- 1 Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University , Durham, North Carolina.,2 Center for Healthy Aging and Development Studies, National School of Development, Peking University , Beijing, China
| | - Huashuai Chen
- 1 Center for the Study of Aging and Human Development and Geriatrics Division, Medical School of Duke University , Durham, North Carolina.,3 Department of Management, Business School of Xiangtan University , Xiangtan, China
| | - Ting Ni
- 4 State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai, China
| | - Rongping Ruan
- 5 Department of Agriculture Economics. Renmin University of China , Beijing, China
| | - Chao Nie
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China
| | - Xiaomin Liu
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China
| | - Lei Feng
- 7 Department of Psychological Medicine, National University of Singapore , Singapore
| | - Fengyu Zhang
- 8 Lieber Institute for Brain Development, Johns Hopkins University , Baltimore, Maryland
| | - Jiehua Lu
- 9 Department of Sociology, Peking University , Beijing, China
| | - Jianxin Li
- 9 Department of Sociology, Peking University , Beijing, China
| | - Yang Li
- 10 Department of Human Population Genetics, Institute of Molecular Medicine, Peking University , Beijing, China
| | - Wei Tao
- 11 School of Life Sciences, Peking University , Beijing, China
| | - Simon G Gregory
- 12 Duke Molecular Physiology Institute, Duke University , Durham, North Carolina
| | - William Gottschalk
- 13 Department of Neurology, Medical Center, Duke University , Durham, North Carolina
| | - Michael W Lutz
- 13 Department of Neurology, Medical Center, Duke University , Durham, North Carolina
| | - Kenneth C Land
- 14 Population Research Institute, Duke University , Durham, North Carolina
| | - Anatoli Yashin
- 14 Population Research Institute, Duke University , Durham, North Carolina
| | - Qihua Tan
- 15 Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark , Odense, Denmark
| | - Ze Yang
- 16 National Institute of Geriatrics, Beijing Hospital , Ministry of Health of China, Beijing, China
| | - Lars Bolund
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China .,17 Department of Biomedicine, Aarhus University , Aarhus, Denmark
| | - Qi Ming
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China .,18 Center for Genetic & Genomic Medicine, Zhejiang University School of Medicine , Hangzhou, China
| | - Huanming Yang
- 6 Beijing Genomics Institute (BGI)-Shenzhen , Shenzhen, China .,19 James D. Watson Institute of Genome Sciences , Hangzhou, China .,20 Princess Al-Jawhara Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Junxia Min
- 21 School of Medicine, Zhejiang University , Hangzhou, China
| | - D Craig Willcox
- 22 Department of Human Welfare, Okinawa International University , Ginowan, Japan .,23 Department of Research, Kuakini Medical Center and Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii , Hawaii
| | - Bradley J Willcox
- 23 Department of Research, Kuakini Medical Center and Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii , Hawaii
| | - Jun Gu
- 11 School of Life Sciences, Peking University , Beijing, China
| | - Elizabeth Hauser
- 12 Duke Molecular Physiology Institute, Duke University , Durham, North Carolina
| | - Xiao-Li Tian
- 10 Department of Human Population Genetics, Institute of Molecular Medicine, Peking University , Beijing, China
| | - James W Vaupel
- 24 Max Planck Institute for Demographic Research , Rostock, Germany
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Kraus WE, Muoio DM, Stevens R, Craig D, Bain JR, Grass E, Haynes C, Kwee L, Qin X, Slentz DH, Krupp D, Muehlbauer M, Hauser ER, Gregory SG, Newgard CB, Shah SH. Metabolomic Quantitative Trait Loci (mQTL) Mapping Implicates the Ubiquitin Proteasome System in Cardiovascular Disease Pathogenesis. PLoS Genet 2015; 11:e1005553. [PMID: 26540294 PMCID: PMC4634848 DOI: 10.1371/journal.pgen.1005553] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/04/2015] [Indexed: 12/15/2022] Open
Abstract
Levels of certain circulating short-chain dicarboxylacylcarnitine (SCDA), long-chain dicarboxylacylcarnitine (LCDA) and medium chain acylcarnitine (MCA) metabolites are heritable and predict cardiovascular disease (CVD) events. Little is known about the biological pathways that influence levels of most of these metabolites. Here, we analyzed genetics, epigenetics, and transcriptomics with metabolomics in samples from a large CVD cohort to identify novel genetic markers for CVD and to better understand the role of metabolites in CVD pathogenesis. Using genomewide association in the CATHGEN cohort (N = 1490), we observed associations of several metabolites with genetic loci. Our strongest findings were for SCDA metabolite levels with variants in genes that regulate components of endoplasmic reticulum (ER) stress (USP3, HERC1, STIM1, SEL1L, FBXO25, SUGT1) These findings were validated in a second cohort of CATHGEN subjects (N = 2022, combined p = 8.4x10-6–2.3x10-10). Importantly, variants in these genes independently predicted CVD events. Association of genomewide methylation profiles with SCDA metabolites identified two ER stress genes as differentially methylated (BRSK2 and HOOK2). Expression quantitative trait loci (eQTL) pathway analyses driven by gene variants and SCDA metabolites corroborated perturbations in ER stress and highlighted the ubiquitin proteasome system (UPS) arm. Moreover, culture of human kidney cells in the presence of levels of fatty acids found in individuals with cardiometabolic disease, induced accumulation of SCDA metabolites in parallel with increases in the ER stress marker BiP. Thus, our integrative strategy implicates the UPS arm of the ER stress pathway in CVD pathogenesis, and identifies novel genetic loci associated with CVD event risk. Cardiovascular disease is a strongly heritable trait. Despite application of the latest genomic technologies, the genetic architecture of disease risk remains poorly defined, and mechanisms underlying this susceptibility are incompletely understood. In this study, we performed genome-wide mapping of heart disease-related metabolites measured in the blood as the genetic traits of interest (instead of the disease itself), in a large cohort of 3512 patients at risk of heart disease from the CATHGEN study. Our goal was to discover new cardiovascular disease genes and thereby mechanisms of disease pathogenesis by understanding the genes that regulate levels of these metabolites. These analyses identified novel genetic variants associated with metabolite levels and with cardiovascular disease itself. Importantly, by utilizing an unbiased systems-based approach integrating genetics, gene expression, epigenetics and metabolomics, we uncovered a novel pathway of heart disease pathogenesis, that of endoplasmic reticulum (ER) stress, represented by elevated levels of circulating short-chain dicarboxylacylcarnitine (SCDA) metabolites.
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Affiliation(s)
- William E. Kraus
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Deborah M. Muoio
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
- Division of Endocrinology, Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Robert Stevens
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Damian Craig
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - James R. Bain
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Elizabeth Grass
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Carol Haynes
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Lydia Kwee
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Xuejun Qin
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Dorothy H. Slentz
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Deidre Krupp
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Michael Muehlbauer
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Christopher B. Newgard
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
| | - Svati H. Shah
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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49
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Ward-Caviness CK, Kraus WE, Blach C, Haynes CS, Dowdy E, Miranda ML, Devlin RB, Diaz-Sanchez D, Cascio WE, Mukerjee S, Stallings C, Smith LA, Gregory SG, Shah SH, Hauser ER, Neas LM. Association of Roadway Proximity with Fasting Plasma Glucose and Metabolic Risk Factors for Cardiovascular Disease in a Cross-Sectional Study of Cardiac Catheterization Patients. Environ Health Perspect 2015; 123:1007-14. [PMID: 25807578 PMCID: PMC4590740 DOI: 10.1289/ehp.1306980] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 03/19/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND The relationship between traffic-related air pollution (TRAP) and risk factors for cardiovascular disease needs to be better understood in order to address the adverse impact of air pollution on human health. OBJECTIVE We examined associations between roadway proximity and traffic exposure zones, as markers of TRAP exposure, and metabolic biomarkers for cardiovascular disease risk in a cohort of patients undergoing cardiac catheterization. METHODS We performed a cross-sectional study of 2,124 individuals residing in North Carolina (USA). Roadway proximity was assessed via distance to primary and secondary roadways, and we used residence in traffic exposure zones (TEZs) as a proxy for TRAP. Two categories of metabolic outcomes were studied: measures associated with glucose control, and measures associated with lipid metabolism. Statistical models were adjusted for race, sex, smoking, body mass index, and socioeconomic status (SES). RESULTS An interquartile-range (990 m) decrease in distance to roadways was associated with higher fasting plasma glucose (β = 2.17 mg/dL; 95% CI: -0.24, 4.59), and the association appeared to be limited to women (β = 5.16 mg/dL; 95% CI: 1.48, 8.84 compared with β = 0.14 mg/dL; 95% CI: -3.04, 3.33 in men). Residence in TEZ 5 (high-speed traffic) and TEZ 6 (stop-and-go traffic), the two traffic zones assumed to have the highest levels of TRAP, was positively associated with high-density lipoprotein cholesterol (HDL-C; β = 8.36; 95% CI: -0.15, 16.9 and β = 5.98; 95% CI: -3.96, 15.9, for TEZ 5 and 6, respectively). CONCLUSION Proxy measures of TRAP exposure were associated with intermediate metabolic traits associated with cardiovascular disease, including fasting plasma glucose and possibly HDL-C.
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Affiliation(s)
- Cavin K Ward-Caviness
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina, USA
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50
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Riley RT, Torres O, Matute J, Gregory SG, Ashley-Koch AE, Showker JL, Mitchell T, Voss KA, Maddox JR, Gelineau-van Waes JB. Evidence for fumonisin inhibition of ceramide synthase in humans consuming maize-based foods and living in high exposure communities in Guatemala. Mol Nutr Food Res 2015; 59:2209-24. [PMID: 26264677 DOI: 10.1002/mnfr.201500499] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 07/31/2015] [Accepted: 08/04/2015] [Indexed: 11/12/2022]
Abstract
SCOPE Fumonisin (FB) occurs in maize and is an inhibitor of ceramide synthase (CerS). We determined the urinary FB1 (UFB1 ) and sphingoid base 1-phosphate levels in blood from women consuming maize in high and low FB exposure communities in Guatemala. METHODS AND RESULTS FB1 intake was estimated using the UFB1 . Sphinganine 1-phosphate (Sa 1-P), sphingosine 1-phosphate (So 1-P), and the Sa 1-P/So 1-P ratio were determined in blood spots collected on absorbent paper at the same time as urine collection. In the first study, blood spots and urine were collected every 3 months (March 2011 to February 2012) from women living in low (Chimaltenango and Escuintla) and high (Jutiapa) FB exposure communities (1240 total recruits). The UFB1 , Sa 1-P/So 1-P ratio, and Sa 1-P/mL in blood spots were significantly higher in the high FB1 intake community compared to the low FB1 intake communities. The results were confirmed in a follow-up study (February 2013) involving 299 women living in low (Sacatepéquez) and high (Santa Rosa and Chiquimula) FB exposure communities. CONCLUSIONS High levels of FB1 intake are correlated with changes in Sa 1-P and the Sa 1-P/So 1-P ratio in human blood in a manner consistent with FB1 inhibition of CerS.
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Affiliation(s)
- Ronald T Riley
- Toxicology and Mycotoxin Research Unit, US National Poultry Research Center, USDA - ARS, R.B. Russell Research Center, Athens, GA, USA
| | - Olga Torres
- Laboratorio Diagnostico Molecular S.A, Guatemala City, Guatemala.,Centro de Investigaciones en Nutrición y Salud, Guatemala City, Guatemala
| | - Jorge Matute
- Centro de Investigaciones en Nutrición y Salud, Guatemala City, Guatemala
| | - Simon G Gregory
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Jency L Showker
- Toxicology and Mycotoxin Research Unit, US National Poultry Research Center, USDA - ARS, R.B. Russell Research Center, Athens, GA, USA
| | - Trevor Mitchell
- Toxicology and Mycotoxin Research Unit, US National Poultry Research Center, USDA - ARS, R.B. Russell Research Center, Athens, GA, USA
| | - Kenneth A Voss
- Toxicology and Mycotoxin Research Unit, US National Poultry Research Center, USDA - ARS, R.B. Russell Research Center, Athens, GA, USA
| | - Joyce R Maddox
- Department of Pharmacology, School of Medicine, Creighton University, Omaha, NE, USA
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