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Tomasi J, Lisoway AJ, Zai CC, Zai G, Richter MA, Sanches M, Herbert D, Mohiuddin AG, Tiwari AK, Kennedy JL. Genetic and polygenic investigation of heart rate variability to identify biomarkers associated with Anxiety disorders. Psychiatry Res 2024; 338:115982. [PMID: 38850888 DOI: 10.1016/j.psychres.2024.115982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/11/2024] [Accepted: 05/26/2024] [Indexed: 06/10/2024]
Abstract
Given that anxiety disorders (AD) are associated with reduced vagally-mediated heart rate variability (HRV), genetic variants related to HRV may provide insight into anxiety etiology. This study used polygenic risk scores (PRS) to explore the genetic overlap between AD and HRV, and investigated whether HRV-related polymorphisms influence anxiety risk. Resting vagally-mediated HRV was measured using a wearable device in 188 European individuals (AD=101, healthy controls=87). AD PRS was tested for association with resting HRV, and HRV PRS for association with AD. We also investigated 15 significant hits from an HRV genome-wide association study (GWAS) for association with resting HRV and AD and if this association is mediated through resting HRV. The AD PRS and HRV PRS showed nominally significant associations with resting HRV and anxiety disorders, respectively. HRV GWAS variants associated with resting HRV were rs12980262 (NDUFA11), rs2680344 (HCN4), rs4262 and rs180238 (GNG11), and rs10842383 (LINC00477). Mediation analyses revealed that NDUFA11 rs12980262 A-carriers and GNG11 rs180238 and rs4262 C-carriers had higher anxiety risk through lower HRV. This study supports an anxiety-HRV genetic relationship, with HRV-related genetic variants translating to AD. This study encourages exploration of HRV genetics to understand mechanisms and identify novel treatment targets for anxiety.
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Affiliation(s)
- Julia Tomasi
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada.
| | - Amanda J Lisoway
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Clement C Zai
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gwyneth Zai
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; General Adult Psychiatry and Health Systems Division, CAMH, Toronto, ON, Canada
| | - Margaret A Richter
- Institute of Medical Science, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Frederick W. Thompson Anxiety Disorders Centre, Department of Psychiatry, Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Marcos Sanches
- Biostatistics Core, Centre for Addiction and Mental Health, Toronto, Canada
| | - Deanna Herbert
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada
| | - Ayeshah G Mohiuddin
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada
| | - Arun K Tiwari
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada.
| | - James L Kennedy
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada
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Kulshrestha P, Sharma S, Vishwakarma S, Ali MJ, Dave TV, Kaur I. Quality and applicability of cadaveric donor eyes for molecular biology research: An Indian experience. Indian J Ophthalmol 2024; 72:962-967. [PMID: 38454856 DOI: 10.4103/ijo.ijo_2553_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/04/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE Human ocular tissue banking plays an important part in the advancement of translational research for identifying the molecular processes involved in disease etiology and pathogenesis. Timely obtaining a good-quality ocular tissue from a cadaveric donor is exceedingly difficult, especially in remote areas, with a variable transportation time (within 12-24 h), raising concerns about RNA quality and its subsequent applications. Therefore, we assessed the utility of retinal tissues from cadaver donor and enucleated eyes based on the RNA quality and gene expression by real-time polymerase chain reaction (PCR). SETTINGS AND DESIGN Prospective study. METHODS Retina tissues were separated from the donor/enucleated eyes received in the eye bank within 24 h of death (n = 15) and within an hour from OR (n = 3), respectively, and stored immediately at -80 degree. RNA was isolated using trizol, and the quantity and quality were assessed using Qubit and agarose gel electrophoresis, respectively. QPCR was performed for measuring the expression of different retinal-specific genes. The cellular viability of the retina was assessed by establishing explant primary cell cultures. STATISTICAL ANALYSIS The data were calculated as an average of normalised Ct values ± standard error of the mean. RESULTS RNA obtained from cadaveric tissues despite being partially degraded showed a uniform strong gene expression of several retinal-specific genes such as PAX6, RHO, TUBB3, CRX , and ALDH1L1 . The primary cultures established from cadaveric tissues showed viable cells. CONCLUSION The cadaver donor tissues collected within 24 hours of death can be effectively utilized for gene expression profiling.
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Affiliation(s)
- Prerna Kulshrestha
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sarmeela Sharma
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sushma Vishwakarma
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mohammed J Ali
- Govindram Seksaria Institute of Dacryology, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Tarjani V Dave
- Hariram Motumal Nasta and Renu Hariram Nasta Ophthalmic Plastic Surgery Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Inderjeet Kaur
- Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
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Andrzejczyk K, Abou Kamar S, van Ommen AM, Canto ED, Petersen TB, Valstar G, Akkerhuis KM, Cramer MJ, Umans V, Rutten FH, Teske A, Boersma E, Menken R, van Dalen BM, Hofstra L, Verhaar M, Brugts J, Asselbergs F, den Ruijter H, Kardys I. Identifying plasma proteomic signatures from health to heart failure, across the ejection fraction spectrum. Sci Rep 2024; 14:14871. [PMID: 38937570 PMCID: PMC11211454 DOI: 10.1038/s41598-024-65667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024] Open
Abstract
Circulating proteins may provide insights into the varying biological mechanisms involved in heart failure (HF) with preserved ejection fraction (HFpEF) and reduced ejection fraction (HFrEF). We aimed to identify specific proteomic patterns for HF, by comparing proteomic profiles across the ejection fraction spectrum. We investigated 4210 circulating proteins in 739 patients with normal (Stage A/Healthy) or elevated (Stage B) filling pressures, HFpEF, or ischemic HFrEF (iHFrEF). We found 2122 differentially expressed proteins between iHFrEF-Stage A/Healthy, 1462 between iHFrEF-HFpEF and 52 between HFpEF-Stage A/Healthy. Of these 52 proteins, 50 were also found in iHFrEF vs. Stage A/Healthy, leaving SLITRK6 and NELL2 expressed in lower levels only in HFpEF. Moreover, 108 proteins, linked to regulation of cell fate commitment, differed only between iHFrEF-HFpEF. Proteomics across the HF spectrum reveals overlap in differentially expressed proteins compared to stage A/Healthy. Multiple proteins are unique for distinguishing iHFrEF from HFpEF, supporting the capacity of proteomics to discern between these conditions.
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Affiliation(s)
- Karolina Andrzejczyk
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sabrina Abou Kamar
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Cardiology, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Anne-Mar van Ommen
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Elisa Dal Canto
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of General Practice & Nursing Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Teun B Petersen
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Biostatistics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gideon Valstar
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - K Martijn Akkerhuis
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Maarten Jan Cramer
- Clinical Cardiology Department, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Victor Umans
- Department of Cardiology, Northwest Clinics, Alkmaar, the Netherlands
| | - Frans H Rutten
- Department of General Practice & Nursing Science, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Arco Teske
- Clinical Cardiology Department, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Eric Boersma
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Roxana Menken
- Cardiology Centers of the Netherlands, Utrecht, The Netherlands
| | - Bas M van Dalen
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Cardiology, Franciscus Gasthuis & Vlietland, Rotterdam, The Netherlands
| | - Leonard Hofstra
- Cardiology Centers of the Netherlands, Utrecht, The Netherlands
| | - Marianne Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jasper Brugts
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Folkert Asselbergs
- Clinical Cardiology Department, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hester den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Clinical Cardiology Department, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Isabella Kardys
- Department of Cardiology, Thorax Center, Cardiovascular Institute, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Du K, Wang L, Jun JH, Dutta RK, Maeso-Díaz R, Oh SH, Ko DC, Diehl AM. Aging promotes metabolic dysfunction-associated steatotic liver disease by inducing ferroptotic stress. NATURE AGING 2024:10.1038/s43587-024-00652-w. [PMID: 38918603 DOI: 10.1038/s43587-024-00652-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
Susceptibility to the biological consequences of aging varies among organs and individuals. We analyzed hepatocyte transcriptomes of healthy young and aged male mice to generate an aging hepatocyte gene signature, used it to deconvolute transcriptomic data from humans and mice with metabolic dysfunction-associated liver disease, validated findings with functional studies in mice and applied the signature to transcriptomic data from other organs to determine whether aging-sensitive degenerative mechanisms are conserved. We discovered that the signature enriches in diseased livers in parallel with degeneration. It is also enriched in failing human hearts, diseased kidneys and pancreatic islets from individuals with diabetes. The signature includes genes that control ferroptosis. Aged mice develop more hepatocyte ferroptosis and liver degeneration than young mice when fed diets that induce metabolic stress. Inhibiting ferroptosis shifts the liver transcriptome of old mice toward that of young mice and reverses aging-exacerbated liver damage, identifying ferroptosis as a tractable, conserved mechanism for aging-related tissue degeneration.
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Affiliation(s)
- Kuo Du
- Department of Medicine, Duke University, Durham, NC, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Ji Hye Jun
- Department of Medicine, Duke University, Durham, NC, USA
| | - Rajesh K Dutta
- Department of Medicine, Duke University, Durham, NC, USA
| | | | - Seh Hoon Oh
- Department of Medicine, Duke University, Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Anna Mae Diehl
- Department of Medicine, Duke University, Durham, NC, USA.
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Jiang J, Hiron TK, Agbaedeng TA, Malhotra Y, Drydale E, Bancroft J, Ng E, Reschen ME, Davison LJ, O’Callaghan CA. A Novel Macrophage Subpopulation Conveys Increased Genetic Risk of Coronary Artery Disease. Circ Res 2024; 135:6-25. [PMID: 38747151 PMCID: PMC11191562 DOI: 10.1161/circresaha.123.324172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Coronary artery disease (CAD), the leading cause of death worldwide, is influenced by both environmental and genetic factors. Although over 250 genetic risk loci have been identified through genome-wide association studies, the specific causal variants and their regulatory mechanisms are still largely unknown, particularly in disease-relevant cell types such as macrophages. METHODS We utilized single-cell RNA-seq and single-cell multiomics approaches in primary human monocyte-derived macrophages to explore the transcriptional regulatory network involved in a critical pathogenic event of coronary atherosclerosis-the formation of lipid-laden foam cells. The relative genetic contribution to CAD was assessed by partitioning disease heritability across different macrophage subpopulations. Meta-analysis of single-cell RNA-seq data sets from 38 human atherosclerotic samples was conducted to provide high-resolution cross-referencing to macrophage subpopulations in vivo. RESULTS We identified 18 782 cis-regulatory elements by jointly profiling the gene expression and chromatin accessibility of >5000 macrophages. Integration with CAD genome-wide association study data prioritized 121 CAD-related genetic variants and 56 candidate causal genes. We showed that CAD heritability was not uniformly distributed and was particularly enriched in the gene programs of a novel CD52-hi lipid-handling macrophage subpopulation. These CD52-hi macrophages displayed significantly less lipoprotein accumulation and were also found in human atherosclerotic plaques. We investigated the cis-regulatory effect of a risk variant rs10488763 on FDX1, implicating the recruitment of AP-1 and C/EBP-β in the causal mechanisms at this locus. CONCLUSIONS Our results provide genetic evidence of the divergent roles of macrophage subsets in atherogenesis and highlight lipid-handling macrophages as a key subpopulation through which genetic variants operate to influence disease. These findings provide an unbiased framework for functional fine-mapping of genome-wide association study results using single-cell multiomics and offer new insights into the genotype-environment interactions underlying atherosclerotic disease.
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Affiliation(s)
- Jiahao Jiang
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Thomas K. Hiron
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Thomas A. Agbaedeng
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Yashaswat Malhotra
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Edward Drydale
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - James Bancroft
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
| | - Esther Ng
- Nuffield Department of Orthopaedics, Kennedy Institute of Rheumatology, Rheumatology and Musculoskeletal Sciences (E.N.), University of Oxford, United Kingdom
| | - Michael E. Reschen
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, United Kingdom (M.E.R.)
| | - Lucy J. Davison
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
- Department of Clinical Science and Services, Royal Veterinary College, Hatfield, United Kingdom (L.J.D.)
| | - Chris A. O’Callaghan
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics (J.J., T.K.H., T.A.A., Y.M., E.D., J.B., L.J.D., C.A.O.), University of Oxford, United Kingdom
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Tatomir A, Vlaicu S, Nguyen V, Luzina IG, Atamas SP, Drachenberg C, Papadimitriou J, Badea TC, Rus HG, Rus V. RGC-32 mediates proinflammatory and profibrotic pathways in immune-mediated kidney disease. Clin Immunol 2024; 265:110279. [PMID: 38878807 DOI: 10.1016/j.clim.2024.110279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
Systemic lupus erythematosus is an autoimmune disease that results in immune-mediated damage to kidneys and other organs. We investigated the role of response gene to complement-32 (RGC-32), a proinflammatory and profibrotic mediator induced by TGFβ and C5b-9, in nephrotoxic nephritis (NTN), an experimental model that mimics human lupus nephritis. Proteinuria, loss of renal function and kidney histopathology were attenuated in RGC-32 KO NTN mice. RGC-32 KO NTN mice displayed downregulation of the CCL20/CCR6 and CXCL9/CXCR3 ligand/receptor pairs resulting in decreased renal recruitment of IL-17+ and IFNγ+ cells and subsequent decrease in the influx of innate immune cells. RGC-32 deficiency attenuated renal fibrosis as demonstrated by decreased deposition of collagen I, III and fibronectin. Thus, RGC-32 is a unique mediator shared by the Th17 and Th1 dependent proinflammatory and profibrotic pathways and a potential novel therapeutic target in the treatment of immune complex mediated glomerulonephritis such as lupus nephritis.
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Affiliation(s)
- Alexandru Tatomir
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA; Neurology Service, Veterans Administration Medical Health Care Center, Baltimore, MD, USA
| | - Sonia Vlaicu
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Internal Medicine, Medical Clinic nr. 1, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Vinh Nguyen
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Irina G Luzina
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sergei P Atamas
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | - Tudor C Badea
- Research and Development Institute, Faculty of Medicine, Transylvania University of Brasov, Brasov, Romania
| | - Horea G Rus
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA; Neurology Service, Veterans Administration Medical Health Care Center, Baltimore, MD, USA
| | - Violeta Rus
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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Sulkava S, Haukka J, Kaivola K, Doagu F, Lahtinen A, Kantojärvi K, Pärn K, Palta P, Myllykangas L, Sulkava R, Laatikainen T, Tienari PJ, Paunio T. Job-related exhaustion risk variant in UST is associated with dementia and DNA methylation. Sci Rep 2024; 14:13668. [PMID: 38871764 PMCID: PMC11176189 DOI: 10.1038/s41598-024-62600-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
Previous genome-wide association and replication study for job-related exhaustion indicated a risk variant, rs13219957 in the UST gene. Epidemiological studies suggest connection of stress-related conditions and dementia risk. Therefore, we first studied association of rs13219957 and register-based incident dementia using survival models in the Finnish National FINRISK study surveys (N = 26,693). The AA genotype of rs13219957 was significantly associated with 40% increased risk of all-cause dementia. Then we analysed the UST locus association with brain pathology in the Vantaa 85+ cohort and found association with tau pathology (Braak stage) but not with amyloid pathology. Finally, in the functional analyses, rs13219957 showed a highly significant association with two DNA methylation sites of UST, and UST expression. Thus, the results suggest a common risk variant for a stress-related condition and dementia. Mechanisms to mediate the connection may include differential DNA methylation and transcriptional regulation of UST.
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Affiliation(s)
- Sonja Sulkava
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, Helsinki University Central Hospital, University of Helsinki , Helsinki, Finland.
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland.
| | - Jari Haukka
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Karri Kaivola
- Translational Immunology Program, Department of Neurology, Brain Centre, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Fatma Doagu
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, Helsinki University Central Hospital, University of Helsinki , Helsinki, Finland
- Neuroscience Center, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Alexandra Lahtinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, Helsinki University Central Hospital, University of Helsinki , Helsinki, Finland
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katri Kantojärvi
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, Helsinki University Central Hospital, University of Helsinki , Helsinki, Finland
| | - Kalle Pärn
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Liisa Myllykangas
- Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Raimo Sulkava
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Amia Memory Clinics, Helsinki, Finland
| | - Tiina Laatikainen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Joint Municipal Authority for North Karelia Social and Health Services (Siun Sote), Joensuu, Finland
| | - Pentti J Tienari
- Translational Immunology Program, Department of Neurology, Brain Centre, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Tiina Paunio
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, Helsinki University Central Hospital, University of Helsinki , Helsinki, Finland
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8
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Gelernter J, Levey DF, Galimberti M, Harrington K, Zhou H, Adhikari K, Gupta P, Gaziano JM, Eliott D, Stein MB. Genome-wide association study of the common retinal disorder epiretinal membrane: Significant risk loci in each of three American populations. CELL GENOMICS 2024; 4:100582. [PMID: 38870908 DOI: 10.1016/j.xgen.2024.100582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/20/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024]
Abstract
Epiretinal membrane (ERM) is a common retinal condition characterized by the presence of fibrocellular tissue on the retinal surface, often with visual distortion and loss of visual acuity. We studied European American (EUR), African American (AFR), and Latino (admixed American, AMR) ERM participants in the Million Veteran Program (MVP) for genome-wide association analysis-a total of 38,232 case individuals and 557,988 control individuals. We completed a genome-wide association study (GWAS) in each population separately, and then results were meta-analyzed. Genome-wide significant (GWS) associations were observed in all three populations studied: 31 risk loci in EUR subjects, 3 in AFR, and 2 in AMR, with 48 in trans-ancestry meta-analysis. Many results replicated in the FinnGen sample. Several GWS variants associate to alterations in gene expression in the macula. ERM showed significant genetic correlation to multiple traits. Pathway enrichment analyses implicated collagen and collagen-adjacent mechanisms, among others. This well-powered ERM GWAS identified novel genetic associations that point to biological mechanisms for ERM.
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Affiliation(s)
- Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, VA Connecticut Healthcare Center, West Haven, CT, USA; Departments of Genetics and Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| | - Daniel F Levey
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Marco Galimberti
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Kelly Harrington
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA; Department of Psychiatry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Hang Zhou
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Keyrun Adhikari
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Priya Gupta
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA; Department of Psychiatry, VA Connecticut Healthcare Center, West Haven, CT, USA
| | - J Michael Gaziano
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Medicine, Divisions of Aging and Preventative Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dean Eliott
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Murray B Stein
- University of California, San Diego, La Jolla, CA, USA; VA San Diego Healthcare System, San Diego, CA, USA
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9
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Fass SB, Mulvey B, Chase R, Yang W, Selmanovic D, Chaturvedi SM, Tycksen E, Weiss LA, Dougherty JD. Relationship between sex biases in gene expression and sex biases in autism and Alzheimer's disease. Biol Sex Differ 2024; 15:47. [PMID: 38844994 PMCID: PMC11157820 DOI: 10.1186/s13293-024-00622-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Sex differences in the brain may play an important role in sex-differential prevalence of neuropsychiatric conditions. METHODS In order to understand the transcriptional basis of sex differences, we analyzed multiple, large-scale, human postmortem brain RNA-Seq datasets using both within-region and pan-regional frameworks. RESULTS We find evidence of sex-biased transcription in many autosomal genes, some of which provide evidence for pathways and cell population differences between chromosomally male and female individuals. These analyses also highlight regional differences in the extent of sex-differential gene expression. We observe an increase in specific neuronal transcripts in male brains and an increase in immune and glial function-related transcripts in female brains. Integration with single-nucleus data suggests this corresponds to sex differences in cellular states rather than cell abundance. Integration with case-control gene expression studies suggests a female molecular predisposition towards Alzheimer's disease, a female-biased disease. Autism, a male-biased diagnosis, does not exhibit a male predisposition pattern in our analysis. CONCLUSION Overall, these analyses highlight mechanisms by which sex differences may interact with sex-biased conditions in the brain. Furthermore, we provide region-specific analyses of sex differences in brain gene expression to enable additional studies at the interface of gene expression and diagnostic differences.
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Affiliation(s)
- Stuart B Fass
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
| | - Bernard Mulvey
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- Lieber Institute for Brain Development, 855 North Wolfe St. Ste 300, Baltimore, MD, 21205, USA
| | - Rebecca Chase
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Din Selmanovic
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
| | - Sneha M Chaturvedi
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
| | - Eric Tycksen
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Lauren A Weiss
- Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Ave, HSE901, San Francisco, CA, 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, 513 Parnassus Ave, HSE901, San Francisco, CA, 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, 513 Parnassus Ave, HSE901, San Francisco, CA, 94143, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA.
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA.
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis, MO, 63110, USA.
- Department of Genetics, 4566 Scott Ave., Campus Box 8232, St. Louis, MO, 63110-1093, USA.
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10
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Weng LC, Khurshid S, Hall AW, Nauffal V, Morrill VN, Sun YV, Rämö JT, Beer D, Lee S, Nadkarni G, Johnson R, Andreasen L, Clayton A, Pullinger CR, Yoneda ZT, Friedman DJ, Hyman MC, Judy RL, Skanes AC, Orland KM, Jordà P, Treu TM, Oetjens MT, Subbiah R, Hartmann JP, May HT, Kane JP, Issa TZ, Nafissi NA, Leong-Sit P, Dubé MP, Roselli C, Choi SH, Tardif JC, Khan HR, Knight S, Svendsen JH, Walker B, Linnér RK, Gaziano JM, Tadros R, Fatkin D, Rader DJ, Shah SH, Roden DM, Marcus GM, Loos RJ, Damrauer SM, Haggerty CM, Cho K, Palotie A, Olesen MS, Eckhardt LL, Roberts JD, Cutler MJ, Shoemaker MB, Wilson PW, Ellinor PT, Lubitz SA. Meta-Analysis of Genome-Wide Association Studies Reveals Genetic Mechanisms of Supraventricular Arrhythmias. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004320. [PMID: 38804128 PMCID: PMC11187659 DOI: 10.1161/circgen.123.004320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/31/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Substantial data support a heritable basis for supraventricular tachycardias, but the genetic determinants and molecular mechanisms of these arrhythmias are poorly understood. We sought to identify genetic loci associated with atrioventricular nodal reentrant tachycardia (AVNRT) and atrioventricular accessory pathways or atrioventricular reciprocating tachycardia (AVAPs/AVRT). METHODS We performed multiancestry meta-analyses of genome-wide association studies to identify genetic loci for AVNRT (4 studies) and AVAP/AVRT (7 studies). We assessed evidence supporting the potential causal effects of candidate genes by analyzing relations between associated variants and cardiac gene expression, performing transcriptome-wide analyses, and examining prior genome-wide association studies. RESULTS Analyses comprised 2384 AVNRT cases and 106 489 referents, and 2811 AVAP/AVRT cases and 1,483 093 referents. We identified 2 significant loci for AVNRT, which implicate NKX2-5 and TTN as disease susceptibility genes. A transcriptome-wide association analysis supported an association between reduced predicted cardiac expression of NKX2-5 and AVNRT. We identified 3 significant loci for AVAP/AVRT, which implicate SCN5A, SCN10A, and TTN/CCDC141. Variant associations at several loci have been previously reported for cardiac phenotypes, including atrial fibrillation, stroke, Brugada syndrome, and electrocardiographic intervals. CONCLUSIONS Our findings highlight gene regions associated with ion channel function (AVAP/AVRT), as well as cardiac development and the sarcomere (AVAP/AVRT and AVNRT) as important potential effectors of supraventricular tachycardia susceptibility.
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Affiliation(s)
- Lu-Chen Weng
- Cardiovascular Rsrch Ctr, Dept of Medicine, Dept of Neurology & Dept of Psychiatry, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
- VA Boston Healthcare System
| | - Shaan Khurshid
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
- Demoulas Ctr for Cardiac Arrhythmias, Dept of Medicine, Dept of Neurology & Dept of Psychiatry, MGH, Boston
| | - Amelia Weber Hall
- Gene Regulation Observatory, The Broad Institute of MIT & Harvard, Cambridge
| | - Victor Nauffal
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
- VA Boston Healthcare System
- Cardiovascular Medicine Division, Brigham and Women’s Hospital, Boston, MA
| | - Valerie N. Morrill
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
| | - Yan V. Sun
- Dept of Epidemiology, Emory Univ Rollins School of Public Health, Atlanta
- VA Atlanta Healthcare System, Decatur, GA
| | - Joel T. Rämö
- Inst for Molecular Medicine Finland (FIMM), Helsinki Inst of Life Science (HiLIFE), Univ of Helsinki, Helsinki, Finland
- The Broad Inst of MIT & Harvard, Cambridge, MA
| | | | - Simon Lee
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Renee Johnson
- Victor Chang Cardiac Rsrch Inst, Darlinghurst
- School of Clinical Medicine, Faculty of Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Laura Andreasen
- Laboratory for Molecular Cardiology, Dept of Cardiology, Copenhagen Univ Hospital, Rigshospitalet
- Dept of Biomedical Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Anne Clayton
- Intermountain Heart Inst, Intermountain Medical Ctr, Murray, UT
| | - Clive R. Pullinger
- Cardiovascular Rsrch Inst & Dept of Physiological Nursing, Univ of California, San Francisco, CA
| | - Zachary T. Yoneda
- Dept of Medicine, Division of Cardiovascular Medicine, Vanderbilt Univ Medical Ctr, Nashville, TN
| | - Daniel J. Friedman
- Division of Cardiology, Dept of Medicine, Duke Univ School of Medicine, Durham, NC
| | - Matthew C. Hyman
- Division of Cardiac Electrophysiology, Hospital of the Univ of Pennsylvania
| | - Renae L. Judy
- Dept of Surgery, Perelman School of Medicine, Univ of Pennsylvania, Philadelphia, PA
| | - Allan C. Skanes
- Section of Cardiac Electrophysiology, Division of Cardiology, Dept of Medicine, Western Univ, London, ON, Canada
| | - Kate M. Orland
- Dept of Medicine, Division of Cardiovascular Medicine, Univ of Wisconsin–Madison, Madison, WI
| | - Paloma Jordà
- Montreal Heart Inst Rsrch Ctr & Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | | | | | - Rajesh Subbiah
- Victor Chang Cardiac Rsrch Inst, Darlinghurst
- School of Clinical Medicine, Faculty of Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
- St Vincent’s Hospital, Darlinghurst
| | - Jacob P. Hartmann
- Laboratory for Molecular Cardiology, Dept of Cardiology, Copenhagen Univ Hospital, Rigshospitalet
| | - Heidi T. May
- Intermountain Heart Inst, Intermountain Medical Ctr, Murray, UT
| | - John P. Kane
- Cardiovascular Rsrch Inst, Univ of California, San Francisco, CA
- Dept of Medicine, Univ of California, San Francisco, CA
- Dept of Biochemistry & Biophysics, Univ of California, San Francisco, CA
| | - Tariq Z. Issa
- Feinberg School of Medicine, Northwestern Univ, Chicago, IL
| | - Navid A. Nafissi
- Division of Cardiology, Dept of Medicine, Duke Univ School of Medicine, Durham, NC
| | - Peter Leong-Sit
- Section of Cardiac Electrophysiology, Division of Cardiology, Dept of Medicine, Western Univ, London, ON, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Inst Rsrch Ctr & Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Beaulieu-Saucier Pharmacogenomics Ctr, Montreal, Canada
| | - Carolina Roselli
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
- Dept of Cardiology, Univ of Groningen, University Medical Ctr Groningen, the Netherlands
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
| | | | | | | | - Jean-Claude Tardif
- Montreal Heart Inst Rsrch Ctr & Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Habib R. Khan
- Section of Cardiac Electrophysiology, Division of Cardiology, Dept of Medicine, Western Univ, London, ON, Canada
| | - Stacey Knight
- Intermountain Heart Inst, Intermountain Medical Ctr, Murray, UT
- Dept of Medicine, Univ of Utah, Salt Lake City, UT
| | - Jesper H. Svendsen
- Laboratory for Molecular Cardiology, Dept of Cardiology, Copenhagen Univ Hospital, Rigshospitalet
- Dept of Clinical Medicine, Univ of Copenhagen, Copenhagen, Denmark
| | - Bruce Walker
- School of Clinical Medicine, Faculty of Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
- St Vincent’s Hospital, Darlinghurst
| | - Richard Karlsson Linnér
- Autism & Developmental Medicine Inst, Geisinger, Lewisburg, PA
- Dept of Economics, Leiden Law School, Leiden Univ, Leiden, the Netherlands
| | - J. Michael Gaziano
- VA Boston Healthcare System
- Cardiovascular Medicine Division, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Rafik Tadros
- Montreal Heart Inst Rsrch Ctr & Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Diane Fatkin
- Victor Chang Cardiac Rsrch Inst, Darlinghurst
- School of Clinical Medicine, Faculty of Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
- St Vincent’s Hospital, Darlinghurst
| | - Daniel J. Rader
- Division of Cardiovascular Medicine, Dept of Medicine, Perelman School of Medicine, Univ of Pennsylvania, Philadelphia, PA
| | - Svati H. Shah
- Division of Cardiology, Dept of Medicine, Duke Univ School of Medicine, Durham, NC
- Duke Molecular Physiology Inst, Duke Univ School of Medicine, Durham, NC
| | | | | | - Ruth J.F. Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY & Novo Nordisk Foundation Ctr for Basic Metabolic Rsrch, Dept of Health & Medical Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Scott M. Damrauer
- Dept of Surgery & Dept of Genetics, Perelman School of Medicine, Univ of Pennsylvania, Philadelphia, PA
- Corporal Michael Crescenz VA Medical Ctr, Philadelphia
| | - Christopher M. Haggerty
- Heart Inst, Geisinger, Danville, PA
- Dept of Translational Data Science & Informatics, Geisinger, Danville, PA
| | - Kelly Cho
- VA Boston Healthcare System
- Cardiovascular Medicine Division, Brigham and Women’s Hospital, Boston, MA
| | - Aarno Palotie
- Inst for Molecular Medicine Finland (FIMM), Helsinki Inst of Life Science (HiLIFE), Univ of Helsinki, Helsinki, Finland
- The Stanley Center for Psychiatric Rsrch & Program in Medical & Population Genetics, The Broad Institute of MIT & Harvard, Cambridge
- Analytic & Translational Genetics Unit, Dept of Medicine, Dept of Neurology & Dept of Psychiatry, MGH, Boston
| | - Morten S. Olesen
- Laboratory for Molecular Cardiology, Dept of Cardiology, Copenhagen Univ Hospital, Rigshospitalet
- Dept of Biomedical Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Lee L. Eckhardt
- Dept of Medicine, Division of Cardiovascular Medicine, Univ of Wisconsin–Madison, Madison, WI
| | - Jason D. Roberts
- Section of Cardiac Electrophysiology, Division of Cardiology, Dept of Medicine, Western Univ, London, ON, Canada
| | | | - M. Benjamin Shoemaker
- Dept of Medicine, Division of Cardiovascular Medicine, Vanderbilt Univ Medical Ctr, Nashville, TN
| | - Peter W.F. Wilson
- VA Atlanta Healthcare System, Decatur, GA
- Dept of Medicine, Emory Univ School of Medicine, Atlanta, GA
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
- Demoulas Ctr for Cardiac Arrhythmias, Dept of Medicine, Dept of Neurology & Dept of Psychiatry, MGH, Boston
| | - Steven A. Lubitz
- Cardiovascular Disease Initiative, The Broad Institute of MIT & Harvard, Cambridge
- Demoulas Ctr for Cardiac Arrhythmias, Dept of Medicine, Dept of Neurology & Dept of Psychiatry, MGH, Boston
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11
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Bravo JI, Mizrahi CR, Kim S, Zhang L, Suh Y, Benayoun BA. An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells. PLoS Genet 2024; 20:e1011311. [PMID: 38848448 PMCID: PMC11189215 DOI: 10.1371/journal.pgen.1011311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 06/20/2024] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Long interspersed element 1 (LINE-1; L1) are a family of transposons that occupy ~17% of the human genome. Though a small number of L1 copies remain capable of autonomous transposition, the overwhelming majority of copies are degenerate and immobile. Nevertheless, both mobile and immobile L1s can exert pleiotropic effects (promoting genome instability, inflammation, or cellular senescence) on their hosts, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSD17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for regulators of transposon RNA levels.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, California, United States of America
| | - Chanelle R. Mizrahi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- USC Gerontology Enriching MSTEM to Enhance Diversity in Aging Program, University of Southern California, Los Angeles, California, United States of America
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, United States of America
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, United States of America
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California, United States of America
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California, United States of America
- USC Stem Cell Initiative, Los Angeles, California, United States of America
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12
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Dai J, Jiang H, Yang Z, Chen C, Tang X. A functional variant of ALDH1A2 is associated with hand osteoarthritis in the Chinese population. Int J Immunogenet 2024; 51:157-163. [PMID: 38441233 DOI: 10.1111/iji.12662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 05/08/2024]
Abstract
Genome-wide association study identified common variants within the ALDH1A2 gene as the susceptible loci of hand osteoarthritis (HOA) in UK and Iceland populations. Located in chromosome 15, ALDH1A2 encodes aldehyde dehydrogenase family 1 member A2, which is an enzyme that catalyses the synthesis of retinoic acid from retinaldehyde. Our purposes were to replicate the association of functional variant in ALDH1A2 with the development of HOA in the Chinese population. Variant rs12915901 of ALDH1A2 was genotyped in 872 HOA patients and 1223 healthy controls. Subchondral bone samples were collected from 40 patients who had undergone a trapeziectomy, and the tissue expression of ALDH1A2 was analysed. The chi-square analysis was used to compare the frequency of genotype and risk allele between the HOA cases and controls. The Student t test was used to compare the mRNA expression of ALDH1A2 between patients with genotype AA/AG and those with genotype GG. The frequency of genotype AA was significantly higher in HOA patients than in the controls (7.6% vs. 5.1%, p = .01). The frequency of allele A was significantly higher in the patients than in the controls (28.9% vs. 24.6%, p = .005). The mRNA expression of ALDH1A2 was 1.31-folds higher in patients with genotype GG than in the patients with genotype AA/AG (0.000617 ± 0.000231 vs. 0.000471 ± 0.000198, p = .04). Variant rs12915901 of ALDH1A2 contributed to the susceptibility of HOA in the Chinese population. Allele A of rs12915901 can add to the risk of HOA possibly via down-regulation of ALDH1A2 expression.
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Affiliation(s)
- Jian Dai
- Department of Orthopedics Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Haitao Jiang
- Department of Orthopedics Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
| | - Zhaoqi Yang
- Postgraduate in Orthopedics Surgery, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chuan Chen
- Department of Orthopedics Surgery, Third People's Hospital of Jiujiang City, Jiujiang, Jiangxi, China
| | - Xiaoming Tang
- Department of Orthopedics Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China
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13
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Mao X, Gu H, Kim D, Kimura Y, Wang N, Xu E, Kumbhar R, Ming X, Wang H, Chen C, Zhang S, Jia C, Liu Y, Bian H, Karuppagounder SS, Akkentli F, Chen Q, Jia L, Hwang H, Lee SH, Ke X, Chang M, Li A, Yang J, Rastegar C, Sriparna M, Ge P, Brahmachari S, Kim S, Zhang S, Shimoda Y, Saar M, Liu H, Kweon SH, Ying M, Workman CJ, Vignali DAA, Muller UC, Liu C, Ko HS, Dawson VL, Dawson TM. Aplp1 interacts with Lag3 to facilitate transmission of pathologic α-synuclein. Nat Commun 2024; 15:4663. [PMID: 38821932 PMCID: PMC11143359 DOI: 10.1038/s41467-024-49016-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
Pathologic α-synuclein (α-syn) spreads from cell-to-cell, in part, through binding to the lymphocyte-activation gene 3 (Lag3). Here we report that amyloid β precursor-like protein 1 (Aplp1) interacts with Lag3 that facilitates the binding, internalization, transmission, and toxicity of pathologic α-syn. Deletion of both Aplp1 and Lag3 eliminates the loss of dopaminergic neurons and the accompanying behavioral deficits induced by α-syn preformed fibrils (PFF). Anti-Lag3 prevents the internalization of α-syn PFF by disrupting the interaction of Aplp1 and Lag3, and blocks the neurodegeneration induced by α-syn PFF in vivo. The identification of Aplp1 and the interplay with Lag3 for α-syn PFF induced pathology deepens our insight about molecular mechanisms of cell-to-cell transmission of pathologic α-syn and provides additional targets for therapeutic strategies aimed at preventing neurodegeneration in Parkinson's disease and related α-synucleinopathies.
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Affiliation(s)
- Xiaobo Mao
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.
| | - Hao Gu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Nanjing Brain Hospital, Nanjing, Jiangsu, 210029, PR China
- Medical College, Yangzhou University, Yangzhou, Jiangsu, 225001, PR China
| | - Donghoon Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Pharmacology, College of Medicine, Dong-A University, 32 Daesin Gongwwon-ro, Seo-gu, Busan, 49201, Republic of Korea
| | - Yasuyoshi Kimura
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ning Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Enquan Xu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ramhari Kumbhar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA
| | - Xiaotian Ming
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Haibo Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Chan Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Anesthesiology, West China Hospital, Sichuan University. The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai, 201210, China
| | - Chunyu Jia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai, 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yuqing Liu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Hetao Bian
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Senthilkumar S Karuppagounder
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Fatih Akkentli
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA
| | - Qi Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Longgang Jia
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Heehong Hwang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Su Hyun Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Xiyu Ke
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Materials Science and Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Michael Chang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Amanda Li
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jun Yang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Cyrus Rastegar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Manjari Sriparna
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Preston Ge
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Picower Institute for Learning and Memory, Cambridge, MA, 02139, USA
- Harvard-MIT MD/PhD Program, Harvard Medical School, Boston, MA, 02115, USA
| | - Saurav Brahmachari
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sangjune Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biological Science and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Shu Zhang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yasushi Shimoda
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomiokamachi, Nagaoka, Niigata, 940-2188, Japan
| | - Martina Saar
- Institute for Pharmacy and Molecular Biotechnology IPMB, Department of Functional Genomics, University of Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Haiqing Liu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Physiology, School of Basic Medical Sciences (Institute of Basic Medical Sciences), Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Sin Ho Kweon
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mingyao Ying
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Hugo W. Moser Research Institute at Kennedy Krieger, 707 North Broadway, Baltimore, MD, 21205, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Ulrike C Muller
- Institute for Pharmacy and Molecular Biotechnology IPMB, Department of Functional Genomics, University of Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai, 201210, China
| | - Han Seok Ko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, 70130-2685, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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14
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Miranda AX, Kemp J, Davidson BA, Bellomo SE, Miranda VE, Manoni A, Marchiò C, Croessmann S, Park BH, Hodges E. Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations. BMC Genomics 2024; 25:519. [PMID: 38802751 PMCID: PMC11129441 DOI: 10.1186/s12864-024-10368-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype. RESULTS In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases. CONCLUSIONS Using our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.
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Affiliation(s)
- Adam X Miranda
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Justin Kemp
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brad A Davidson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Verda E Miranda
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexandra Manoni
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sarah Croessmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ben H Park
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA.
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
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15
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Pauly R, Johnson L, Feltus FA, Casanova EL. Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings. Mol Psychiatry 2024:10.1038/s41380-024-02593-7. [PMID: 38760502 DOI: 10.1038/s41380-024-02593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
Homo sapiens and Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts of Neanderthal-derived DNA in the modern human genome. In the current study, we address the potential roles Neanderthal single nucleotide polymorphisms (SNP) may be playing in autism susceptibility in samples of black non-Hispanic, white Hispanic, and white non-Hispanic people using data from the Simons Foundation Powering Autism Research (SPARK), Genotype-Tissue Expression (GTEx), and 1000 Genomes (1000G) databases. We have discovered that rare variants are significantly enriched in autistic probands compared to race-matched controls. In addition, we have identified 25 rare and common SNPs that are significantly enriched in autism on different ethnic backgrounds, some of which show significant clinical associations. We have also identified other SNPs that share more specific genotype-phenotype correlations but which are not necessarily enriched in autism and yet may nevertheless play roles in comorbid phenotype expression (e.g., intellectual disability, epilepsy, and language regression). These results strongly suggest Neanderthal-derived DNA is playing a significant role in autism susceptibility across major populations in the United States.
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Affiliation(s)
- Rini Pauly
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, 29634, USA
| | - Layla Johnson
- Department of Psychology, Loyola University, New Orleans, New Orleans, LA, 70118, USA
| | - F Alex Feltus
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, 29634, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
- Center for Human Genetics, Clemson University, Clemson, SC, 29634, USA
| | - Emily L Casanova
- Department of Psychology, Loyola University, New Orleans, New Orleans, LA, 70118, USA.
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16
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Brown PA. Genes Differentially Expressed Across Major Arteries Are Enriched in Endothelial Dysfunction-Related Gene Sets: Implications for Relative Inter-artery Atherosclerosis Risk. Bioinform Biol Insights 2024; 18:11779322241251563. [PMID: 38765020 PMCID: PMC11100403 DOI: 10.1177/11779322241251563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/13/2024] [Indexed: 05/21/2024] Open
Abstract
Atherosclerosis differs across major arteries. Although the biological basis is not fully understood, limited evidence of genetic differences has been documented. This study, therefore, was aimed to identify differentially expressed genes between clinically relevant major arteries and investigate their enrichment in endothelial dysfunction-related gene sets. A bioinformatic analysis of publicly available gene-level read counts for coronary, aortic, and tibial arteries was performed. Differential gene expression was conducted with DeSeq2 at a false discovery rate of 0.05. Differentially expressed genes were then subjected to over-representation analysis and active-subnetwork-oriented enrichment analysis, both at a false discovery rate of 0.005. Enriched terms common to both analyses were categorized for each contrast into immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related terms, and the top differentially expressed genes validated against Swiss Institute of Bioinformatics' Bgee database. There was mostly upregulation of differentially expressed genes for the coronary/tibial and aorta/tibial contrasts, but milder changes for the coronary/aorta contrast. Transcriptomic differences between coronary or aortic versus tibial samples largely involved immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related genes, suggesting potential to modulate endothelial dysfunction and atherosclerosis. These results imply atheroprone coronary and aortic environments compared with tibial artery tissue, which may explain observed relative inter-artery atherosclerosis risk.
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Affiliation(s)
- Paul A Brown
- Department of Basic Medical Sciences, Faculty of Medical Sciences Teaching and Research Complex, The University of the West Indies, Kingston, Jamaica
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17
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O'Connell GC, Smothers CG, Wang J, Ruksakulpiwat S, Armentrout BL. Brain Expression Levels of Commonly Measured Blood Biomarkers of Neurological Damage Differ with Respect to Sex, Race, and Age. Neuroscience 2024; 551:79-93. [PMID: 38762083 DOI: 10.1016/j.neuroscience.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
It is increasingly evident that blood biomarkers have potential to improve the diagnosis and management of both acute and chronic neurological conditions. The most well-studied candidates, and arguably those with the broadest utility, are proteins that are highly enriched in neural tissues and released into circulation upon cellular damage. It is currently unknown how the brain expression levels of these proteins is influenced by demographic factors such as sex, race, and age. Given that source tissue abundance is likely a key determinant of the levels observed in the blood during neurological pathology, understanding such influences is important in terms of identifying potential clinical scenarios that could produce diagnostic bias. In this study, we leveraged existing mRNA sequencing data originating from 2,642 normal brain specimens harvested from 382 human donors to examine potential demographic variability in the expression levels of genes which code for 28 candidate blood biomarkers of neurological damage. Existing mass spectrometry data originating from 26 additional normal brain specimens harvested from 26 separate human donors was subsequently used to tentatively assess whether observed transcriptional variance was likely to produce corresponding variance in terms of protein abundance. Genes associated with several well-studied or emerging candidate biomarkers including neurofilament light chain (NfL), ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCH-L1), neuron-specific enolase (NSE), and synaptosomal-associated protein 25 (SNAP-25) exhibited significant differences in expression with respect to sex, race, and age. In many instances, these differences in brain expression align well with and provide a mechanistic explanation for previously reported differences in blood levels.
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Affiliation(s)
- Grant C O'Connell
- Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA.
| | | | - Jing Wang
- Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA
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18
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Van R, Alvarez D, Mize T, Gannavarapu S, Chintham Reddy L, Nasoz F, Han MV. A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies. BMC Bioinformatics 2024; 25:181. [PMID: 38720247 PMCID: PMC11080237 DOI: 10.1186/s12859-024-05801-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND RNA sequencing combined with machine learning techniques has provided a modern approach to the molecular classification of cancer. Class predictors, reflecting the disease class, can be constructed for known tissue types using the gene expression measurements extracted from cancer patients. One challenge of current cancer predictors is that they often have suboptimal performance estimates when integrating molecular datasets generated from different labs. Often, the quality of the data is variable, procured differently, and contains unwanted noise hampering the ability of a predictive model to extract useful information. Data preprocessing methods can be applied in attempts to reduce these systematic variations and harmonize the datasets before they are used to build a machine learning model for resolving tissue of origins. RESULTS We aimed to investigate the impact of data preprocessing steps-focusing on normalization, batch effect correction, and data scaling-through trial and comparison. Our goal was to improve the cross-study predictions of tissue of origin for common cancers on large-scale RNA-Seq datasets derived from thousands of patients and over a dozen tumor types. The results showed that the choice of data preprocessing operations affected the performance of the associated classifier models constructed for tissue of origin predictions in cancer. CONCLUSION By using TCGA as a training set and applying data preprocessing methods, we demonstrated that batch effect correction improved performance measured by weighted F1-score in resolving tissue of origin against an independent GTEx test dataset. On the other hand, the use of data preprocessing operations worsened classification performance when the independent test dataset was aggregated from separate studies in ICGC and GEO. Therefore, based on our findings with these publicly available large-scale RNA-Seq datasets, the application of data preprocessing techniques to a machine learning pipeline is not always appropriate.
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Affiliation(s)
- Richard Van
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Daniel Alvarez
- Department of Computer Science, University of Nevada Las Vegas, Las Vegas, NV, USA
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Travis Mize
- Icahn School of Medicine at Mount Sinai, Institute for Genomic Health, New York City, NY, USA
| | - Sravani Gannavarapu
- Department of Computer Science, University of Nevada Las Vegas, Las Vegas, NV, USA
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Lohitha Chintham Reddy
- Department of Computer Science, University of Nevada Las Vegas, Las Vegas, NV, USA
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Fatma Nasoz
- Department of Computer Science, University of Nevada Las Vegas, Las Vegas, NV, USA
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Mira V Han
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA.
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19
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Huang Q, Trumpff C, Monzel AS, Rausser S, Haahr R, Devine J, Liu CC, Kelly C, Thompson E, Kurade M, Michelson J, Shaulson ED, Li S, Engelstad K, Tanji K, Lauriola V, Wang T, Wang S, Zuraikat FM, St-Onge MP, Kaufman BA, Sloan R, Juster RP, Marsland AL, Gouspillou G, Hirano M, Picard M. Psychobiological regulation of plasma and saliva GDF15 dynamics in health and mitochondrial diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590241. [PMID: 38659958 PMCID: PMC11042343 DOI: 10.1101/2024.04.19.590241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
GDF15 (growth differentiation factor 15) is a marker of cellular energetic stress linked to physical-mental illness, aging, and mortality. However, questions remain about its dynamic properties and measurability in human biofluids other than blood. Here, we examine the natural dynamics and psychobiological regulation of plasma and saliva GDF15 in four human studies representing 4,749 samples from 188 individuals. We show that GDF15 protein is detectable in saliva (8% of plasma concentration), likely produced by salivary glands secretory duct cells. Using a brief laboratory socio-evaluative stressor paradigm, we find that psychosocial stress increases plasma (+3.5-5.9%) and saliva GDF15 (+43%) with distinct kinetics, within minutes. Moreover, saliva GDF15 exhibits a robust awakening response, declining by ~40-89% within 30-45 minutes from its peak level at the time of waking up. Clinically, individuals with genetic mitochondrial OxPhos diseases show elevated baseline plasma and saliva GDF15, and post-stress GDF15 levels in both biofluids correlate with multi-system disease severity, exercise intolerance, and the subjective experience of fatigue. Taken together, our data establish that saliva GDF15 is dynamic, sensitive to psychological states, a clinically relevant endocrine marker of mitochondrial diseases. These findings also point to a shared psychobiological pathway integrating metabolic and mental stress.
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Affiliation(s)
- Qiuhan Huang
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Caroline Trumpff
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna S Monzel
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Shannon Rausser
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Rachel Haahr
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Jack Devine
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Cynthia C Liu
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Catherine Kelly
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Elizabeth Thompson
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Mangesh Kurade
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Jeremy Michelson
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Evan D Shaulson
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Shufang Li
- Department of Neurology, H. Houston Merritt Center, Neuromuscular Medicine Division, Columbia University Medical Center, New York, NY, USA
| | - Kris Engelstad
- Department of Neurology, H. Houston Merritt Center, Neuromuscular Medicine Division, Columbia University Medical Center, New York, NY, USA
| | - Kurenai Tanji
- Department of Neurology, H. Houston Merritt Center, Neuromuscular Medicine Division, Columbia University Medical Center, New York, NY, USA
- Department of pathology and cell biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Lauriola
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Tian Wang
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, United States
| | - Shuang Wang
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, United States
| | - Faris M Zuraikat
- Division of General Medicine and Center of Excellence for Sleep & Circadian Research, Department of Medicine, Columbia University Irving Medical Center, New York, USA
| | - Marie-Pierre St-Onge
- Division of General Medicine and Center of Excellence for Sleep & Circadian Research, Department of Medicine, Columbia University Irving Medical Center, New York, USA
| | - Brett A Kaufman
- Department of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Richard Sloan
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert-Paul Juster
- Department of Psychiatry and Addiction, University of Montreal, Montreal, QC, Canada
| | - Anna L Marsland
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Gilles Gouspillou
- Département des Sciences de l'Activité Physique, Faculté des Sciences, UQAM, Montréal, Québec, Canada
| | - Michio Hirano
- Department of Neurology, H. Houston Merritt Center, Neuromuscular Medicine Division, Columbia University Medical Center, New York, NY, USA
| | - Martin Picard
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, H. Houston Merritt Center, Neuromuscular Medicine Division, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA
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20
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Chen PC, Chen WH, Lien LM, Chou CC, Chao CC, Bai CH. Association of IL-18 gene polymorphisms with clinical aspects of hyperlipidemia in middle-aged and early people in the community. Int J Med Sci 2024; 21:1064-1071. [PMID: 38774744 PMCID: PMC11103393 DOI: 10.7150/ijms.90341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 03/16/2024] [Indexed: 05/24/2024] Open
Abstract
Hyperlipidemia is notorious for causing coronary artery disease (CAD). IL-18 is a proinflammtory cytokine that contributes to the pathogenesis of CAD. Previous reports have revealed that genetic polymorphism of IL-18 is associated with its expression level as well as the susceptibility to CAD. In the present study, we aim to investigate the relationship between IL-18 single nucleotide polymorphisms (SNPs) and hyperlipidemia in the Han Chinese population in Taiwan. A total of 580 participants older than 30 were recruited from the community. We collected the demographics, self-reported disease histories, and lifestyles. We also assessed the levels of lipid profiles including total cholesterol (CHOL), triglyceride, low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol. Two SNPs, rs3882891C/A (intron 5) and rs1946518A/C (promoter -607) of IL-18 were elucidated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods. Our results revealed that rs3882891 AA was associated with lower risk of hypercholesterolemia, higher CHOL and LDL-C in subjects (p=0.003, p=0.000 and p=0.005 separately), and rs1946518 CC was associated with hypercholesterolemia, higher CHOL and LDL-C as well (p=0.021, p=0.003 and p=0.001 separately) Furthermore, both SNPs were associated with IL-18 expression level, which was examined by Genotype-Tissue Expression (GTEx) Portal (p=0.042 and 0.016 separately). Finally, the haplotype of IL-18 was subsequently arranged in the order of rs3882891 and rs1946518. The result revealed that the AC haplotype of 2 IL-18 SNPs was also associated with lower risk of hypercholesterolemia, lower levels of CHOL and LDL-C (p=0.01, p=0.001 and 0.003). The current study is the first to report the association between IL-18 SNPs and hyperlipidemia in the Chinese Han population.
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Affiliation(s)
- Po-Chun Chen
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Translational medicine center, Shin-Kong Wu Ho-Su Memorial Hospital, Taipei City, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Wei-Hung Chen
- Department of Neurology, Shin Kong Wu Ho-Su Memorial Hospital, Taipei 111045, Taiwan
| | - Li-Ming Lien
- School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Neurology, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Chia-Chi Chou
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100025, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Internal Medicine, Chang Gung Memorial Hospital, Keelung 204201, Taiwan
| | - Chia-Chia Chao
- Department of Respiratory Therapy, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chyi-Huey Bai
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
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21
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Nuechterlein N, Shelbourn A, Szulzewsky F, Arora S, Casad M, Pattwell S, Merino-Galan L, Sulman E, Arowa S, Alvinez N, Jung M, Brown D, Tang K, Jackson S, Stoica S, Chittaboina P, Banasavadi-Siddegowda YK, Wirsching HG, Stella N, Shapiro L, Paddison P, Patel AP, Gilbert MR, Abdullaev Z, Aldape K, Pratt D, Holland EC, Cimino PJ. Haploinsufficiency of phosphodiesterase 10A activates PI3K/AKT signaling independent of PTEN to induce an aggressive glioma phenotype. Genes Dev 2024; 38:273-288. [PMID: 38589034 PMCID: PMC11065166 DOI: 10.1101/gad.351350.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
Glioblastoma is universally fatal and characterized by frequent chromosomal copy number alterations harboring oncogenes and tumor suppressors. In this study, we analyzed exome-wide human glioblastoma copy number data and found that cytoband 6q27 is an independent poor prognostic marker in multiple data sets. We then combined CRISPR-Cas9 data, human spatial transcriptomic data, and human and mouse RNA sequencing data to nominate PDE10A as a potential haploinsufficient tumor suppressor in the 6q27 region. Mouse glioblastoma modeling using the RCAS/tv-a system confirmed that Pde10a suppression induced an aggressive glioma phenotype in vivo and resistance to temozolomide and radiation therapy in vitro. Cell culture analysis showed that decreased Pde10a expression led to increased PI3K/AKT signaling in a Pten-independent manner, a response blocked by selective PI3K inhibitors. Single-nucleus RNA sequencing from our mouse gliomas in vivo, in combination with cell culture validation, further showed that Pde10a suppression was associated with a proneural-to-mesenchymal transition that exhibited increased cell adhesion and decreased cell migration. Our results indicate that glioblastoma patients harboring PDE10A loss have worse outcomes and potentially increased sensitivity to PI3K inhibition.
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Affiliation(s)
- Nicholas Nuechterlein
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Allison Shelbourn
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Michelle Casad
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Siobhan Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Leyre Merino-Galan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Erik Sulman
- Department of Radiation Oncology, New York University Grossman School of Medicine, New York, New York 11220, USA
| | - Sumaita Arowa
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Neriah Alvinez
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Miyeon Jung
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Desmond Brown
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kayen Tang
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Sadhana Jackson
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Stefan Stoica
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Prashant Chittaboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Yeshavanth K Banasavadi-Siddegowda
- Molecular and Therapeutics Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital, University of Zurich, Zurich 8091, Switzerland
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Linda Shapiro
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Patrick Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina 27710, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA;
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22
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Yu X, Chen Y, Chen J, Fan Y, Lu H, Wu D, Xu Y. Shared genetic architecture between autoimmune disorders and B-cell acute lymphoblastic leukemia: insights from large-scale genome-wide cross-trait analysis. BMC Med 2024; 22:161. [PMID: 38616254 PMCID: PMC11017616 DOI: 10.1186/s12916-024-03385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND To study the shared genetic structure between autoimmune diseases and B-cell acute lymphoblastic leukemia (B-ALL) and identify the shared risk loci and genes and genetic mechanisms involved. METHODS Based on large-scale genome-wide association study (GWAS) summary-level data sets, we observed genetic overlaps between autoimmune diseases and B-ALL, and cross-trait pleiotropic analysis was performed to detect shared pleiotropic loci and genes. A series of functional annotation and tissue-specific analysis were performed to determine the influence of pleiotropic genes. The heritability enrichment analysis was used to detect crucial immune cells and tissues. Finally, bidirectional Mendelian randomization (MR) methods were utilized to investigate the casual associations. RESULTS Our research highlighted shared genetic mechanisms between seven autoimmune disorders and B-ALL. A total of 73 pleiotropic loci were identified at the genome-wide significance level (P < 5 × 10-8), 16 of which had strong evidence of colocalization. We demonstrated that several loci have been previously reported (e.g., 17q21) and discovered some novel loci (e.g., 10p12, 5p13). Further gene-level identified 194 unique pleiotropic genes, for example IKZF1, GATA3, IKZF3, GSDMB, and ORMDL3. Pathway analysis determined the key role of cellular response to cytokine stimulus, B cell activation, and JAK-STAT signaling pathways. SNP-level and gene-level tissue enrichment suggested that crucial role pleiotropic mechanisms involved in the spleen, whole blood, and EBV-transformed lymphocytes. Also, hyprcoloc and stratified LD score regression analyses revealed that B cells at different developmental stages may be involved in mechanisms shared between two different diseases. Finally, two-sample MR analysis determined causal effects of asthma and rheumatoid arthritis on B-ALL. CONCLUSIONS Our research proved shared genetic architecture between autoimmune disorders and B-ALL and shed light on the potential mechanism that might involve in.
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Affiliation(s)
- Xinghao Yu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Yiyin Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Jia Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Fan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huimin Lu
- Department of Outpatient and Emergency, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
| | - Yang Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
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23
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Li JL, Jain N, Tamayo LI, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL. The association of cigarette smoking with DNA methylation and gene expression in human tissue samples. Am J Hum Genet 2024; 111:636-653. [PMID: 38490207 PMCID: PMC11023923 DOI: 10.1016/j.ajhg.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Cigarette smoking adversely affects many aspects of human health, and epigenetic responses to smoking may reflect mechanisms that mediate or defend against these effects. Prior studies of smoking and DNA methylation (DNAm), typically measured in leukocytes, have identified numerous smoking-associated regions (e.g., AHRR). To identify smoking-associated DNAm features in typically inaccessible tissues, we generated array-based DNAm data for 916 tissue samples from the GTEx (Genotype-Tissue Expression) project representing 9 tissue types (lung, colon, ovary, prostate, blood, breast, testis, kidney, and muscle). We identified 6,350 smoking-associated CpGs in lung tissue (n = 212) and 2,735 in colon tissue (n = 210), most not reported previously. For all 7 other tissue types (sample sizes 38-153), no clear associations were observed (false discovery rate 0.05), but some tissues showed enrichment for smoking-associated CpGs reported previously. For 1,646 loci (in lung) and 22 (in colon), smoking was associated with both DNAm and local gene expression. For loci detected in both lung and colon (e.g., AHRR, CYP1B1, CYP1A1), top CpGs often differed between tissues, but similar clusters of hyper- or hypomethylated CpGs were observed, with hypomethylation at regulatory elements corresponding to increased expression. For lung tissue, 17 hallmark gene sets were enriched for smoking-associated CpGs, including xenobiotic- and cancer-related gene sets. At least four smoking-associated regions in lung were impacted by lung methylation quantitative trait loci (QTLs) that co-localize with genome-wide association study (GWAS) signals for lung function (FEV1/FVC), suggesting epigenetic alterations can mediate the effects of smoking on lung health. Our multi-tissue approach has identified smoking-associated regions in disease-relevant tissues, including effects that are shared across tissue types.
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Affiliation(s)
- James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Niyati Jain
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lizeth I Tamayo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Genomics Research Center, AbbVie, North Chicago, IL 60064, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, University of Chicago, Chicago, IL 60637, USA.
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24
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Li D, Li X, Lv J, Li S. Creation of signatures and identification of molecular subtypes based on disulfidptosis-related genes for glioblastoma patients' prognosis and immunological activity. Asian J Surg 2024:S1015-9584(24)00299-9. [PMID: 38462406 DOI: 10.1016/j.asjsur.2024.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/23/2023] [Accepted: 02/02/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND In recent times, disulfidptosis, an intricate form of cellular demise, has garnered attention due to its impact on prognosis, tumor progression and treatment response. Nevertheless, the exact significance of disulfidptosis-related genes (DisRGs) in glioblastoma (GBM) remains enigmatic. METHODS The GEO and TCGA databases provided transcriptional and clinically relevant data on tumor samples, while the GTEx database provided data on healthy tissues. Disulfidptosis-related genes (DisRGs) were procured from previous scholarly investigations. The expression profile of DisRGs was initially scrutinized among patients diagnosed with GBM, subsequent to which their prognostic value was explored. Through consensus clustering, we constructed DisRGs-related clusters and gene subtypes. Our results established that the DisRG-related clusters had differentially expressed genes, resulting in a DisulfidptosisScore model, which had a positive prognostic value. RESULTS The differential expression profile of 24 DisRGs between GBM samples and healthy samples was acquired. Through consensus cluster analysis, two distinct disulfidptosis subtypes, namely DisRGcluster A and DisRGcluster B, were identified. Then, the DisulfidptosisScore model including 4 characteristic genes was constructed.Notably, patients with GBM assigned with lower score demonstrated a considerably longer overall survival (OS) compared to those with higher score. CONCLUSION We have effectively devised a prognostic model associated with disulfidptosis, presenting autonomous prognostic predictions for patients with GBM. These findings serve as a valuable addition to the current comprehension of disulfidptosis and offer fresh theoretical substantiation for the development of enhanced treatment strategies.
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Affiliation(s)
- Dongjun Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, No.39 Huaxiang Road, Tiexi District, Shenyang, 110000, Liaoning, People's Republic of China
| | - Xiaodong Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, No.39 Huaxiang Road, Tiexi District, Shenyang, 110000, Liaoning, People's Republic of China
| | - Jianfeng Lv
- Department of Neurosurgery, Shengjing Hospital of China Medical University, No.39 Huaxiang Road, Tiexi District, Shenyang, 110000, Liaoning, People's Republic of China
| | - Shaoyi Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, No.39 Huaxiang Road, Tiexi District, Shenyang, 110000, Liaoning, People's Republic of China.
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25
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Song Y, Guo J, Zhou Y, Wei X, Li J, Zhang G, Wang H. A loss-of-function variant in ZCWPW1 causes human male infertility with sperm head defect and high DNA fragmentation. Reprod Health 2024; 21:18. [PMID: 38310235 PMCID: PMC10837985 DOI: 10.1186/s12978-024-01746-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/23/2024] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Male infertility is a global health issue. The more causative genes related to human male infertility should be further explored. The essential role of Zcwpw1 in male mouse fertility has been established and the role of ZCWPW1 in human reproduction needs further investigation to verify. METHODS An infertile man with oligoasthenoteratozoospermia phenotype and his parents were recruited from West China Second University Hospital, Sichuan University. A total of 200 healthy Han Chinese volunteers without any evidence of infertility were recruited as normal controls, while an additional 150 infertile individuals were included to assess the prevalence of ZCWPW1 variants in a sporadic male sterile population. The causative gene variant was identified by Whole-exome sequencing and Sanger sequencing. The phenotype of the oligoasthenoteratozoospermia was determined by Papanicolaou staining, immunofluorescence staining and electron microscope. In-vitro experiments, western blot and in-silicon analysis were applied to assess the pathogenicity of the identified variant. Additionally, we examined the influence of the variant on the DNA fragmentation and DNA repair capability by Sperm Chromatin Dispersion and Neutral Comet Assay. RESULTS The proband exhibits a phenotype of oligoasthenoteratozoospermia, his spermatozoa show head defects by semen examination, Papanicolaou staining and electron microscope assays. Whole-exome sequencing and Sanger sequencing found the proband carries a homozygous ZCWPW1 variant (c.1064C > T, p. P355L). Immunofluorescence analysis shows a significant decrease in ZCWPW1 expression in the proband's sperm. By exogenous expression with ZCWPW1 mutant plasmid in vitro, the obvious declined expression of ZCWPW1 with the mutation is validated in HEK293T. After being treated by hydroxyurea, MUT-ZCWPW1 transfected cells and empty vector transfected cells have a higher level of γ-H2AX, increased tail DNA and reduced H3K9ac level than WT-ZCWPW1 transfected cells. Furthermore, the Sperm Chromatin Dispersion assay revealed the proband's spermatozoa have high DNA fragmentation. CONCLUSIONS It is the first report that a novel homozygous missense mutation in ZCWPW1 caused human male infertility with sperm head defects and high DNA fragmentation. This finding enriches the gene variant spectrum and etiology of oligoasthenoteratozoospermia.
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Affiliation(s)
- Yuelin Song
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Juncen Guo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yanling Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xingjian Wei
- Department of Obstetrics and Gynaecology, Southwest Medical University, Luzhou, 646000, China
| | - Jianlan Li
- Child Healthcare Department, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610000, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Guohui Zhang
- Key Laboratory of Reproductive Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610000, China.
| | - Hongjing Wang
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
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26
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Kurtenbach S, Sanchez MI, Kuznetsoff J, Rodriguez DA, Weich N, Dollar JJ, Cruz A, Kurtenbach S, Field MG, Durante MA, Decatur C, Sorouri M, Lai F, Yenisehirli G, Fang B, Shiekhattar R, Pelaez D, Correa ZM, Verdun RE, Harbour JW. PRAME induces genomic instability in uveal melanoma. Oncogene 2024; 43:555-565. [PMID: 38030788 PMCID: PMC10873199 DOI: 10.1038/s41388-023-02887-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
PRAME is a CUL2 ubiquitin ligase subunit that is normally expressed in the testis but becomes aberrantly overexpressed in many cancer types in association with aneuploidy and metastasis. Here, we show that PRAME is expressed predominantly in spermatogonia around the time of meiotic crossing-over in coordination with genes mediating DNA double strand break repair. Expression of PRAME in somatic cells upregulates pathways involved in meiosis, chromosome segregation and DNA repair, and it leads to increased DNA double strand breaks, telomere dysfunction and aneuploidy in neoplastic and non-neoplastic cells. This effect is mediated at least in part by ubiquitination of SMC1A and altered cohesin function. PRAME expression renders cells susceptible to inhibition of PARP1/2, suggesting increased dependence on alternative base excision repair pathways. These findings reveal a distinct oncogenic function of PRAME that can be targeted therapeutically in cancer.
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Affiliation(s)
- Stefan Kurtenbach
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret I Sanchez
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffim Kuznetsoff
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Daniel A Rodriguez
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Natalia Weich
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - James J Dollar
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Anthony Cruz
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sarah Kurtenbach
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Michael A Durante
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Christina Decatur
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mahsa Sorouri
- Department of Ophthalmology and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Fan Lai
- School of Life Sciences, Yunnan University, Kunming, China
| | - Gulum Yenisehirli
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, The Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Daniel Pelaez
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Zelia M Correa
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ramiro E Verdun
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J William Harbour
- Department of Ophthalmology and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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27
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Caldas P, Luz M, Baseggio S, Andrade R, Sobral D, Grosso AR. Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features. Commun Biol 2024; 7:100. [PMID: 38225287 PMCID: PMC10789751 DOI: 10.1038/s42003-024-05779-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Transcription termination is a crucial step in the production of conforming mRNAs and functional proteins. Under cellular stress conditions, the transcription machinery fails to identify the termination site and continues transcribing beyond gene boundaries, a phenomenon designated as transcription readthrough. However, the prevalence and impact of this phenomenon in healthy human tissues remain unexplored. Here, we assessed transcription readthrough in almost 3000 transcriptome profiles representing 23 human tissues and found that 34% of the expressed protein-coding genes produced readthrough transcripts. The production of readthrough transcripts was restricted in genomic regions with high transcriptional activity and was associated with inefficient splicing and increased chromatin accessibility in terminal regions. In addition, we showed that these transcripts contained several binding sites for the same miRNA, unravelling a potential role as miRNA sponges. Overall, this work provides evidence that transcription readthrough is pervasive and non-stochastic, not only in abnormal conditions but also in healthy tissues. This suggests a potential role for such transcripts in modulating normal cellular functions.
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Affiliation(s)
- Paulo Caldas
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Mariana Luz
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Simone Baseggio
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Rita Andrade
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Daniel Sobral
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Ana Rita Grosso
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
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Li S, Spitz N, Ghantous A, Abrishamcar S, Reimann B, Marques I, Silver MJ, Aguilar-Lacasaña S, Kitaba N, Rezwan FI, Röder S, Sirignano L, Tuhkanen J, Mancano G, Sharp GC, Metayer C, Morimoto L, Stein DJ, Zar HJ, Alfano R, Nawrot T, Wang C, Kajantie E, Keikkala E, Mustaniemi S, Ronkainen J, Sebert S, Silva W, Vääräsmäki M, Jaddoe VWV, Bernstein RM, Prentice AM, Cosin-Tomas M, Dwyer T, Håberg SE, Herceg Z, Magnus MC, Munthe-Kaas MC, Page CM, Völker M, Gilles M, Send T, Witt S, Zillich L, Gagliardi L, Richiardi L, Czamara D, Räikkönen K, Chatzi L, Vafeiadi M, Arshad SH, Ewart S, Plusquin M, Felix JF, Moore SE, Vrijheid M, Holloway JW, Karmaus W, Herberth G, Zenclussen A, Streit F, Lahti J, Hüls A, Hoang TT, London SJ, Wiemels JL. A Pregnancy and Childhood Epigenetics Consortium (PACE) meta-analysis highlights potential relationships between birth order and neonatal blood DNA methylation. Commun Biol 2024; 7:66. [PMID: 38195839 PMCID: PMC10776586 DOI: 10.1038/s42003-023-05698-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
Higher birth order is associated with altered risk of many disease states. Changes in placentation and exposures to in utero growth factors with successive pregnancies may impact later life disease risk via persistent DNA methylation alterations. We investigated birth order with Illumina DNA methylation array data in each of 16 birth cohorts (8164 newborns) with European, African, and Latino ancestries from the Pregnancy and Childhood Epigenetics Consortium. Meta-analyzed data demonstrated systematic DNA methylation variation in 341 CpGs (FDR adjusted P < 0.05) and 1107 regions. Forty CpGs were located within known quantitative trait loci for gene expression traits in blood, and trait enrichment analysis suggested a strong association with immune-related, transcriptional control, and blood pressure regulation phenotypes. Decreasing fertility rates worldwide with the concomitant increased proportion of first-born children highlights a potential reflection of birth order-related epigenomic states on changing disease incidence trends.
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Affiliation(s)
- Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Natalia Spitz
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Sarina Abrishamcar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brigitte Reimann
- Centre for Environmental Sciences, UHasselt, Agoralaan, Building D, 3590, Diepenbeek, Belgium
| | - Irene Marques
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Sofía Aguilar-Lacasaña
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Negusse Kitaba
- Human Development and Health, Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
- Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3DB, UK
| | - Stefan Röder
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research -UFZ, Leipzig, Germany
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Johanna Tuhkanen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Giulia Mancano
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- School of Psychology, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Dan J Stein
- SAMRC Unit on Risk & Resilience in Mental Disorders, Dept of Psychiatry & Neuroscience Institute, University of Cape Town, Rondebosch, South Africa
| | - Heather J Zar
- SAMRC Unit on Risk & Resilience in Mental Disorders, Dept of Psychiatry & Neuroscience Institute, University of Cape Town, Rondebosch, South Africa
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Rondebosch, South Africa
| | - Rossella Alfano
- Centre for Environmental Sciences, UHasselt, Agoralaan, Building D, 3590, Diepenbeek, Belgium
| | - Tim Nawrot
- Centre for Environmental Sciences, UHasselt, Agoralaan, Building D, 3590, Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, UHasselt, Agoralaan, Building D, 3590, Diepenbeek, Belgium
| | - Eero Kajantie
- Clinical Medicine Research Unit, Medical Research Center Oulu, Oulu University, Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Pediatric Research Centre, Children's Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Elina Keikkala
- Clinical Medicine Research Unit, Medical Research Center Oulu, Oulu University, Hospital and University of Oulu, Oulu, Finland
- Population Health Unit, Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Oulu, Finland
| | - Sanna Mustaniemi
- Clinical Medicine Research Unit, Medical Research Center Oulu, Oulu University, Hospital and University of Oulu, Oulu, Finland
- Population Health Unit, Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Oulu, Finland
| | - Justiina Ronkainen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Sylvain Sebert
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Wnurinham Silva
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Marja Vääräsmäki
- Clinical Medicine Research Unit, Medical Research Center Oulu, Oulu University, Hospital and University of Oulu, Oulu, Finland
- Population Health Unit, Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Oulu, Finland
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Robin M Bernstein
- Department of Anthropology and Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
| | - Andrew M Prentice
- MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Marta Cosin-Tomas
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Terence Dwyer
- Nuffield Department of Women's & Reproductive Health, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Siri Eldevik Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Monica Cheng Munthe-Kaas
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Norwegian Institute of Public Health, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Physical Health and Aging, Division for Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Maja Völker
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maria Gilles
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Tabea Send
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Stephanie Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Luigi Gagliardi
- Woman and Child Health Department, Ospedale Versilia, AUSL Toscana Nord Ovest, Pisa, Italy
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin, CPO Piemonte, Turin, Italy
| | - Darina Czamara
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Lida Chatzi
- Department of Population and Public Health Sciences, Keck School of Medicine of USC. University of Southern California, Los Angeles, CA, USA
| | - Marina Vafeiadi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Michelle Plusquin
- Centre for Environmental Sciences, UHasselt, Agoralaan, Building D, 3590, Diepenbeek, Belgium
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sophie E Moore
- Department of Women & Children's Health, King's College London, London, UK
| | - Martine Vrijheid
- ISGlobal, Institute for Global Health, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN, USA
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research -UFZ, Leipzig, Germany
| | - Ana Zenclussen
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research -UFZ, Leipzig, Germany
- Perinatal Immunology, Medical Faculty, Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
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Zagkos L, Dib MJ, Cronjé HT, Elliott P, Dehghan A, Tzoulaki I, Gill D, Daghlas I. Cerebrospinal Fluid C1-Esterase Inhibitor and Tie-1 Levels Affect Cognitive Performance: Evidence from Proteome-Wide Mendelian Randomization. Genes (Basel) 2024; 15:71. [PMID: 38254961 PMCID: PMC10815381 DOI: 10.3390/genes15010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
OBJECTIVE The association of cerebrospinal fluid (CSF) protein levels with cognitive function in the general population remains largely unexplored. We performed Mendelian randomization (MR) analyses to query which CSF proteins may have potential causal effects on cognitive performance. METHODS AND ANALYSIS Genetic associations with CSF proteins were obtained from a genome-wide association study conducted in up to 835 European-ancestry individuals and for cognitive performance from a meta-analysis of GWAS including 257,841 European-ancestry individuals. We performed Mendelian randomization (MR) analyses to test the effect of randomly allocated variation in 154 genetically predicted CSF protein levels on cognitive performance. Findings were validated by performing colocalization analyses and considering cognition-related phenotypes. RESULTS Genetically predicted C1-esterase inhibitor levels in the CSF were associated with a better cognitive performance (SD units of cognitive performance per 1 log-relative fluorescence unit (RFU): 0.23, 95% confidence interval: 0.12 to 0.35, p = 7.91 × 10-5), while tyrosine-protein kinase receptor Tie-1 (sTie-1) levels were associated with a worse cognitive performance (-0.43, -0.62 to -0.23, p = 2.08 × 10-5). These findings were supported by colocalization analyses and by concordant effects on distinct cognition-related and brain-volume measures. CONCLUSIONS Human genetics supports a role for the C1-esterase inhibitor and sTie-1 in cognitive performance.
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Affiliation(s)
- Loukas Zagkos
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2BX, UK; (P.E.); (A.D.); (I.T.); (D.G.)
| | - Marie-Joe Dib
- Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Héléne T. Cronjé
- Department of Public Health, Section of Epidemiology, University of Copenhagen, 1165 Copenhagen, Denmark;
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2BX, UK; (P.E.); (A.D.); (I.T.); (D.G.)
- UK Dementia Research Institute at Imperial College London, Hammersmith Hospital, London W1T 7NF, UK
- Medical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2BX, UK; (P.E.); (A.D.); (I.T.); (D.G.)
- UK Dementia Research Institute at Imperial College London, Hammersmith Hospital, London W1T 7NF, UK
- Medical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2BX, UK; (P.E.); (A.D.); (I.T.); (D.G.)
- UK Dementia Research Institute at Imperial College London, Hammersmith Hospital, London W1T 7NF, UK
- Medical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London SW7 2AZ, UK
- Centre for Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London SW7 2BX, UK; (P.E.); (A.D.); (I.T.); (D.G.)
| | - Iyas Daghlas
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA;
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30
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Miranda AX, Kemp J, Davidson B, Bellomo SE, Agan V, Manoni A, Marchiò C, Croessmann S, Park BH, Hodges E. Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.574067. [PMID: 38260414 PMCID: PMC10802285 DOI: 10.1101/2024.01.03.574067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype. Results In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases. Conclusions Using our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.
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Affiliation(s)
- Adam X. Miranda
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Justin Kemp
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brad Davidson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Verda Agan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexandra Manoni
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
- Department of Medical Sciences, University of Turin
| | - Sarah Croessmann
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ben H. Park
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
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31
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Mou SI, Sultana T, Chatterjee D, Faruk MO, Hosen MI. Comprehensive characterization of coding and non-coding single nucleotide polymorphisms of the Myoneurin (MYNN) gene using molecular dynamics simulation and docking approaches. PLoS One 2024; 19:e0296361. [PMID: 38165846 PMCID: PMC10760682 DOI: 10.1371/journal.pone.0296361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024] Open
Abstract
Genome-wide association studies (GWAS) identified a coding single nucleotide polymorphism, MYNN rs10936599, at chromosome 3q. MYNN gene encodes myoneurin protein, which has been associated with several cancer pathogenesis and disease development processes. However, there needed to be a more detailed characterization of this polymorphism's (and other coding and non-coding polymorphisms) structural, functional, and molecular impact. The current study addressed this gap and analyzed different properties of rs10936599 and non-coding SNPs of MYNN via a thorough computational method. The variant, rs10936599, was predicted functionally deleterious by nine functionality prediction approaches, like SIFT, PolyPhen-2, and REVEL, etc. Following that, structural modifications were estimated through the HOPE server and Mutation3D. Moreover, the mutation was found in a conserved and active residue, according to ConSurf and CPORT. Further, the secondary structures were predicted, followed by tertiary structures, and there was a significant deviation between the native and variant models. Similarly, molecular simulation also showed considerable differences in the dynamic pattern of the wildtype and mutant structures. Molecular docking revealed that the variant binds with better docking scores with ligand NOTCH2. In addition to that, non-coding SNPs located at the MYNN locus were retrieved from the ENSEMBL database. These were found to disrupt the transcription factor binding regulatory regions; nonetheless, only two affect miRNA target sites. Again, eight non-coding variants were detected in the testes with normalized expression, whereas HaploReg v4.1 unveiled annotations for non-coding variants. In summary, in silico comprehensive characterization of coding and non-coding single nucleotide polymorphisms of MYNN gene will assist researchers to work on MYNN gene and establish their association with certain types of cancers.
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Affiliation(s)
- Sadia Islam Mou
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tamanna Sultana
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md. Omar Faruk
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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32
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Autio MI, Motakis E, Perrin A, Bin Amin T, Tiang Z, Do DV, Wang J, Tan J, Ding SSL, Tan WX, Lee CJM, Teo AKK, Foo RSY. Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells. eLife 2024; 13:e79592. [PMID: 38164941 PMCID: PMC10836832 DOI: 10.7554/elife.79592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites in vitro using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easy targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.
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Affiliation(s)
- Matias I Autio
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Singapore, Singapore
| | - Efthymios Motakis
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Arnaud Perrin
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Talal Bin Amin
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Singapore, Singapore
| | - Zenia Tiang
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Dang Vinh Do
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Jiaxu Wang
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, Singapore, Singapore
| | - Joanna Tan
- Center for Genome Diagnostics, Genome Institute of Singapore, Singapore, Singapore
| | - Shirley Suet Lee Ding
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Wei Xuan Tan
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chang Jie Mick Lee
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Precision Medicine Translational Research Programme, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Roger S Y Foo
- Laboratory of Molecular Epigenomics and Chromatin Organization, Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, Singapore, Singapore
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33
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Edris A, Voorhies K, Lutz SM, Iribarren C, Hall I, Wu AC, Tobin M, Fawcett K, Lahousse L. Asthma exacerbations and eosinophilia in the UK Biobank: a genome-wide association study. ERJ Open Res 2024; 10:00566-2023. [PMID: 38196893 PMCID: PMC10772900 DOI: 10.1183/23120541.00566-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/31/2023] [Indexed: 01/11/2024] Open
Abstract
Background Asthma exacerbations reflect disease severity, affect morbidity and mortality, and may lead to declining lung function. Inflammatory endotypes (e.g. T2-high (eosinophilic)) may play a key role in asthma exacerbations. We aimed to assess whether genetic susceptibility underlies asthma exacerbation risk and additionally tested for an interaction between genetic variants and eosinophilia on exacerbation risk. Methods UK Biobank data were used to perform a genome-wide association study of individuals with asthma and at least one exacerbation compared to individuals with asthma and no history of exacerbations. Individuals with asthma were identified using self-reported data, hospitalisation data and general practitioner records. Exacerbations were identified as either asthma-related hospitalisation, general practitioner record of asthma exacerbation or an oral corticosteroid burst prescription. A logistic regression model adjusted for age, sex, smoking status and genetic ancestry via principal components was used to assess the association between genetic variants and asthma exacerbations. We sought replication for suggestive associations (p<5×10-6) in the GERA cohort. Results In the UK Biobank, we identified 11 604 cases and 37 890 controls. While no variants reached genome-wide significance (p<5×10-8) in the primary analysis, 116 signals were suggestively significant (p<5×10-6). In GERA, two single nucleotide polymorphisms (rs34643691 and rs149721630) replicated (p<0.05), representing signals near the NTRK3 and ABCA13 genes. Conclusions Our study has identified reproducible associations with asthma exacerbations in the UK Biobank and GERA cohorts. Confirmation of these findings in different asthma subphenotypes in diverse ancestries and functional investigation will be required to understand their mechanisms of action and potentially inform therapeutic development.
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Affiliation(s)
- Ahmed Edris
- Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Kirsten Voorhies
- Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Sharon M. Lutz
- Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Ian Hall
- Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Ann Chen Wu
- Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Martin Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Katherine Fawcett
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
- These authors contributed equally
| | - Lies Lahousse
- Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
- These authors contributed equally
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Liang J, LaFleur B, Hussainy S, Perry G. Gene Co-Expression Analysis of Multiple Brain Tissues Reveals Correlation of FAM222A Expression with Multiple Alzheimer's Disease-Related Genes. J Alzheimers Dis 2024; 99:S249-S263. [PMID: 37092222 PMCID: PMC11091573 DOI: 10.3233/jad-221241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/25/2023]
Abstract
Background Alzheimer's disease (AD) is the most common form of dementia in the elderly marked by central nervous system (CNS) neuronal loss and amyloid plaques. FAM222A, encoding an amyloid plaque core protein, is an AD brain atrophy susceptibility gene that mediates amyloid-β aggregation. However, the expression interplay between FAM222A and other AD-related pathway genes is unclear. Objective Our goal was to study FAM222A's whole-genome co-expression profile in multiple tissues and investigate its interplay with other AD-related genes. Methods We analyzed gene expression correlations in Genotype-Tissue Expression (GTEx) tissues to identify FAM222A co-expressed genes and performed functional enrichment analysis on identified genes in CNS system. Results Genome-wide gene expression profiling identified 673 genes significantly correlated with FAM222A (p < 2.5×10-6) in 48 human tissues, including 298 from 13 CNS tissues. Functional enrichment analysis revealed that FAM222A co-expressed CNS genes were enriched in multiple AD-related pathways. Gene co-expression network analysis for identified genes in each brain region predicted other disease associated genes with similar biological function. Furthermore, co-expression of 25 out of 31 AD-related pathways genes with FAM222A was replicated in brain samples from 107 aged subjects from the Aging, Dementia and TBI Study. Conclusion This gene co-expression study identified multiple AD-related genes that are associated with FAM222A, indicating that FAM222A and AD-associated genes can be active simultaneously in similar biological processes, providing evidence that supports the association of FAM222A with AD.
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Affiliation(s)
- Jingjing Liang
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - Bonnie LaFleur
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - Sadiya Hussainy
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | - George Perry
- College of Sciences, University of Texas at San Antonio, San Antonio, TX, USA
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Máčová L, Kancheva R, Bičíková M. Molecular Regulation of the CNS by Vitamin D. Physiol Res 2023; 72:S339-S356. [PMID: 38116771 DOI: 10.33549/physiolres.935248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
Vitamin D is a lipid-soluble vitamin that can be found in some foods. It is also produced endogenously (in the presence of ultraviolet light), transported through the blood to the targets organs and this is the reason to consider vitamin D as a hormone. It is known that vitamin D has genomic and non-genomic effects. This review is focused mainly on the vitamin D receptors, the importance of vitamin D as a neuromodulator, the role of vitamin D in the pathophysiology of devastating neurological disorders such as Alzheimer's disease, multiple sclerosis, amyotrophic lateral sclerosis, Parkinson's disease and the benefit of vitamin D and its derivates in alleviating these disorders.
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Affiliation(s)
- L Máčová
- Department of Steroids and Proteofactors, Institute of Endocrinology, Prague, Czech Republic
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Santana-da-Silva MN, Sena-dos-Santos C, Cáceres-Durán MÁ, de Souza FG, Gobbo AR, Pinto P, Salgado CG, dos Santos SEB. ncRNAs: an unexplored cellular defense mechanism in leprosy. Front Genet 2023; 14:1295586. [PMID: 38116294 PMCID: PMC10729009 DOI: 10.3389/fgene.2023.1295586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Leprosy is an infectious disease primarily caused by the obligate intracellular parasite Mycobacterium leprae. Although it has been considered eradicated in many countries, leprosy continues to be a health issue in developing nations. Besides the social stigma associated with it, individuals affected by leprosy may experience nerve damage leading to physical disabilities if the disease is not properly treated or early diagnosed. Leprosy is recognized as a complex disease wherein socioenvironmental factors, immune response, and host genetics interact to contribute to its development. Recently, a new field of study called epigenetics has emerged, revealing that the immune response and other mechanisms related to infectious diseases can be influenced by noncoding RNAs. This review aims to summarize the significant advancements concerning non-coding RNAs in leprosy, discussing the key perspectives on this novel approach to comprehending the pathophysiology of the disease and identifying molecular markers. In our view, investigations on non-coding RNAs in leprosy hold promise and warrant increased attention from researches in this field.
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Affiliation(s)
- Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Imunologia, Seção de Virologia (SAVIR), Instituto Evandro Chagas, Ananindeua, Brazil
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Angelica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Sidney Emanuel Batista dos Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
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Bravo JI, Mizrahi CR, Kim S, Zhang L, Suh Y, Benayoun BA. An eQTL-based Approach Reveals Candidate Regulators of LINE-1 RNA Levels in Lymphoblastoid Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553416. [PMID: 37645920 PMCID: PMC10461994 DOI: 10.1101/2023.08.15.553416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Long interspersed element 1 (L1) are a family of autonomous, actively mobile transposons that occupy ~17% of the human genome. A number of pleiotropic effects induced by L1 (promoting genome instability, inflammation, or cellular senescence) have been observed, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSDB17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for transposon transcriptional regulators.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Chanelle R. Mizrahi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Gerontology Enriching MSTEM to Enhance Diversity in Aging Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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Dack K, Bustamante M, Taylor CM, Llop S, Lozano M, Yousefi P, Gražulevičienė R, Gutzkow KB, Brantsæter AL, Mason D, Escaramís G, Lewis SJ. Genome-Wide Association Study of Blood Mercury in European Pregnant Women and Children. Genes (Basel) 2023; 14:2123. [PMID: 38136945 PMCID: PMC10742428 DOI: 10.3390/genes14122123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Mercury has high industrial utility and is present in many products, and environmental contamination and occupational exposure are widespread. There are numerous biological systems involved in the absorption, metabolism, and excretion of Hg, and it is possible that some systems may be impacted by genetic variation. If so, genotype may affect tissue concentrations of Hg and subsequent toxic effects. Genome-wide association testing was performed on blood Hg samples from pregnant women of the Avon Longitudinal Study of Parents and Children (n = 2893) and children of the Human Early Life Exposome (n = 1042). Directly-genotyped single-nucleotide polymorphisms (SNPs) were imputed to the Haplotype Reference Consortium r1.1 panel of whole genotypes and modelled againstlog-transformed Hg. Heritability was estimated using linkage disequilibrium score regression. The heritability of Hg was estimated as 24.0% (95% CI: 16.9% to 46.4%) in pregnant women, but could not be determined in children. There were 16 SNPs associated with Hg in pregnant women above a suggestive p-value threshold (p < 1 × 10-5), and 21 for children. However, no SNP passed this threshold in both studies, and none were genome-wide significant (p < 5 × 10-8). SNP-Hg associations were highly discordant between women and children, and this may reflect differences in metabolism, a gene-age interaction, or dose-response effects. Several suggestive variants had plausible links to Hg metabolism, such as rs146099921 in metal transporter SLC39A14, and two variants (rs28618224, rs7154700) in potassium voltage-gated channel genes. The findings would benefit from external validation, as suggestive results may contain both true associations and false positives.
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Affiliation(s)
- Kyle Dack
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, UK; (K.D.)
| | - Mariona Bustamante
- ISGlobal, Institute for Global Health, 08036 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain (G.E.)
| | - Caroline M. Taylor
- Centre for Academic Child Health, Bristol Medical School, University of Bristol, Bristol BS8 2PS, UK;
| | - Sabrina Llop
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain (G.E.)
- Epidemiology and Environmental Health Joint Research Unit, FISABIO- Universitat Jaume I - Universitat de València, 46020 Valencia, Spain
| | - Manuel Lozano
- Epidemiology and Environmental Health Joint Research Unit, FISABIO- Universitat Jaume I - Universitat de València, 46020 Valencia, Spain
- Department of Preventative Medicine, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, 46100 Valencia, Spain
| | - Paul Yousefi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, UK; (K.D.)
| | - Regina Gražulevičienė
- Department of Environmental Sciences, Faculty of Natural Sciences, Vytautas Magnus University, 53361 Kaunas, Lithuania
| | - Kristine Bjerve Gutzkow
- Department of Air Quality and Noise, Division of Climate and Environmental Health, Norwegian Institute of Public Health, P.O. Box 222 Skoyen, NO-0213 Oslo, Norway;
| | - Anne Lise Brantsæter
- Department of Food Safety, Division of Climate and Environmental Health, Norwegian Institute of Public Health, P.O. Box 222 Skoyen, NO-0213 Oslo, Norway
| | - Dan Mason
- Bradford Teaching Hospitals NHS Foundation Trust, Duckworth Lane, Bradford BD9 6RJ, UK
| | - Georgia Escaramís
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain (G.E.)
- Department of Biomedical Sciences, Institute of Neuroscience, University of Barcelona, 08035 Barcelona, Spain
| | - Sarah J. Lewis
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1TH, UK; (K.D.)
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1TH, UK
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Tsuyuzaki K, Ishii M, Nikaido I. Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. BMC Bioinformatics 2023; 24:420. [PMID: 37936079 PMCID: PMC10631077 DOI: 10.1186/s12859-023-05490-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/21/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand-receptor (L-R) gene co-expression but the analytical methods are not appropriate to detect many-to-many CCIs. RESULTS In this work, we propose scTensor, a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L-R pairs. CONCLUSIONS Through extensive studies with simulated and empirical datasets, we have shown that scTensor can detect some hypergraphs that cannot be detected using conventional CCI detection methods, especially when they include many-to-many relationships. scTensor is implemented as a freely available R/Bioconductor package.
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Affiliation(s)
- Koki Tsuyuzaki
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Japan Science and Technology Agency, PRESTO, 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.
| | - Manabu Ishii
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Department of Functional Genome Informatics, Division of Biological Data Science, Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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Bustos MA, Yokoe T, Shoji Y, Kobayashi Y, Mizuno S, Murakami T, Zhang X, Sekhar SC, Kim S, Ryu S, Knarr M, Vasilev SA, DiFeo A, Drapkin R, Hoon DSB. MiR-181a targets STING to drive PARP inhibitor resistance in BRCA- mutated triple-negative breast cancer and ovarian cancer. Cell Biosci 2023; 13:200. [PMID: 37932806 PMCID: PMC10626784 DOI: 10.1186/s13578-023-01151-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Poly (ADP-ribose) polymerase inhibitors (PARPi) are approved for the treatment of BRCA-mutated breast cancer (BC), including triple-negative BC (TNBC) and ovarian cancer (OvCa). A key challenge is to identify the factors associated with PARPi resistance; although, previous studies suggest that platinum-based agents and PARPi share similar resistance mechanisms. METHODS Olaparib-resistant (OlaR) cell lines were analyzed using HTG EdgeSeq miRNA Whole Transcriptomic Analysis (WTA). Functional assays were performed in three BRCA-mutated TNBC cell lines. In-silico analysis were performed using multiple databases including The Cancer Genome Atlas, the Genotype-Tissue Expression, The Cancer Cell Line Encyclopedia, Genomics of Drug Sensitivity in Cancer, and Gene Omnibus Expression. RESULTS High miR-181a levels were identified in OlaR TNBC cell lines (p = 0.001) as well as in tumor tissues from TNBC patients (p = 0.001). We hypothesized that miR-181a downregulates the stimulator of interferon genes (STING) and the downstream proinflammatory cytokines to mediate PARPi resistance. BRCA1 mutated TNBC cell lines with miR-181a-overexpression were more resistant to olaparib and showed downregulation in STING and the downstream genes controlled by STING. Extracellular vesicles derived from PARPi-resistant TNBC cell lines horizontally transferred miR-181a to parental cells which conferred PARPi-resistance and targeted STING. In clinical settings, STING levels were positively correlated with interferon gamma (IFNG) response scores (p = 0.01). In addition, low IFNG response scores were associated with worse response to neoadjuvant treatment including PARPi for high-risk HER2 negative BC patients (p = 0.001). OlaR TNBC cell lines showed resistance to platinum-based drugs. OvCa cell lines resistant to platinum showed resistance to olaparib. Knockout of miR-181a significantly improved olaparib sensitivity in OvCa cell lines (p = 0.001). CONCLUSION miR-181a is a key factor controlling the STING pathway and driving PARPi and platinum-based drug resistance in TNBC and OvCa. The miR-181a-STING axis can be used as a potential marker for predicting PARPi responses in TNBC and OvCa tumors.
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Affiliation(s)
- Matias A Bustos
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Takamichi Yokoe
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Yoshiaki Shoji
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Yuta Kobayashi
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Shodai Mizuno
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Tomohiro Murakami
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Xiaoqing Zhang
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA
| | - Sreeja C Sekhar
- Department of Obstetrics & Gynecology, University Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, Rogel Cancer Center, University Michigan, Ann Arbor, MI, 48109, USA
| | - SooMin Kim
- Department of Genome Sequencing, SJCI at Providence SJHC, Santa Monica, CA, 90404, USA
| | - Suyeon Ryu
- Department of Genome Sequencing, SJCI at Providence SJHC, Santa Monica, CA, 90404, USA
| | - Matthew Knarr
- Department of Obstetrics and Gynecology, Perelman School of Medicine, Penn Ovarian Cancer Research Center, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Steven A Vasilev
- Department of Gynecologic Oncology Research, SJCI at SJHC, Santa Monica, CA, 90404, USA
| | - Analisa DiFeo
- Department of Obstetrics & Gynecology, University Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, Rogel Cancer Center, University Michigan, Ann Arbor, MI, 48109, USA
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology, Perelman School of Medicine, Penn Ovarian Cancer Research Center, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint John's Cancer Institute (SJCI) at Providence Saint John's Health Center (SJHC), 2200 Santa Monica Blvd, Santa Monica, CA, 90404, USA.
- Department of Genome Sequencing, SJCI at Providence SJHC, Santa Monica, CA, 90404, USA.
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Nevalainen T, Autio A, Hurme M. Human endogenous retroviruses of the HERV-K (HML-2) family are expressed in the brain of healthy individuals and modify the composition of the brain-infiltrating immune cells. Heliyon 2023; 9:e21283. [PMID: 37920490 PMCID: PMC10618496 DOI: 10.1016/j.heliyon.2023.e21283] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/10/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections in the human genome. RNA expression of individual HERVs has frequently been observed in various pathologic conditions, but some activity can also be seen in healthy individuals, e.g. in the blood. To quantitate the basal expression levels of HERVs in the brain, we now used high-throughput sequencing-based metagenomic analysis to characterize the expression profiles of the HERV-K (HML-2) family proviruses in different brain regions of healthy brain tissue. To this end, RNA-seq data from the Genotype-Tissue Expression (GTEx) project was used. The GTEx project is a public resource to study tissue-specific gene expression and regulation, consisting of a large selection of sequenced samples from different tissues. The GTEx data used in this study consisted of 378 samples taken from 13 brain regions from 55 individuals. The data demonstrated that out of 99 intact proviruses in the family 58 were expressed, but the expression profiles were highly divergent and there were no significant differences in the expression profiles between the various anatomic regions of the brain. It is known that the brain contains a variety of infiltrating immune cells, which are probably of great importance both in the normal defense mechanisms as well as in the various pathogenic processes. Digital cytometry (CIBERSORTx) was used to quantify the proportions of the infiltrating immune cells in the same brain samples. Six most abundant (>5 % of the total population) cell types were observed to be CD4 memory resting T cells, M0 macrophages, plasma cells, CD8 T cells, CD4 memory activated T cells, and monocytes. Analysis of the correlations between the individual HERVs and infiltrating cell types indicated that a cluster of 6 HERVs had a notable correlation signature between T cell type infiltrating cell proportions and HERV RNA expression intensity. The correlations between inflammatory type infiltrating cells were negative or weak. Taken together, these data indicate that the expression of HERVs is associated with a T cell type immunity.
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Affiliation(s)
- Tapio Nevalainen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
- Tampere University Hospital, Finland
| | - Arttu Autio
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
| | - Mikko Hurme
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere, Finland
- Tampere University Hospital, Finland
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Collins JM, Wang D. A Comprehensive Evaluation of the Effects of RNA-Editing Proteins ADAR and ADARB1 on the Expression of the Drug-Metabolizing Enzymes in HepaRG Cells. Drug Metab Dispos 2023; 51:1508-1514. [PMID: 37532539 PMCID: PMC10586505 DOI: 10.1124/dmd.123.001396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023] Open
Abstract
Two RNA-editing proteins, the adenosine deaminase acting on RNA, ADAR, and ADARB1, broadly regulate gene expression in editing-dependent and editing-independent manners. Previous studies showed that the expression of the drug-metabolizing cytochrome P450s (P450s) and UDP glucuronosyltransferases (UGTs) changes upon knockdown (KD) of ADAR or ADARB1 in different hepatic cell lines. To systematically survey the effects of these two ADARs on the expression of P450s and UGTs, we used small interfering RNA in HepaRG cells and tested the association between the expression of the P450s and ADARs in a liver sample cohort (n = 246). KD of ADAR increased the expression of the CYP3As and CYP2C9 and reduced the expression of the others, whereas KD of ADARB1 reduced the expression of nearly all genes tested. ADAR KD also suppressed the induction of most P450s, whereas ADARB1 KD had mixed effects depending on the inducer/gene combination. P450 expression was positively associated with both ADARs in liver samples, consistent with the KD results. However, after adjusting for the expression of transcription factors (TFs) known to regulate P450 expression, the associations disappeared, indicating that the effects of ADAR or ADARB1 primarily occur through TFs. Moreover, we found that the expression of normally spliced CYP3A5 transcripts is increased in both KDs, indicating a direct effect of the ADARs on promoting the usage of the cryptic splice site generated by CYP3A5*3. Taken together, our results revealed the nonoverlapping regulatory effects of ADAR and ADARB1 and supported their broad roles in controlling the expression of drug-metabolizing enzymes in the liver. SIGNIFICANCE STATEMENT: Here, this study systematically surveyed the roles of ADAR and ADARB1 in both basal and induced expression of drug-metabolizing enzymes and assessed their coexpression in liver samples. This study's results support that ADAR and ADARB1 regulate the expression of the drug-metabolizing enzymes in the liver, suggesting that factors affecting ADAR expression also have the potential to impact drug metabolism.
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Affiliation(s)
- Joseph M Collins
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for Pharmacogenomics, University of Florida, Gainesville, Florida
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for Pharmacogenomics, University of Florida, Gainesville, Florida
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Gao T, Kastriti ME, Ljungström V, Heinzel A, Tischler AS, Oberbauer R, Loh PR, Adameyko I, Park PJ, Kharchenko PV. A pan-tissue survey of mosaic chromosomal alterations in 948 individuals. Nat Genet 2023; 55:1901-1911. [PMID: 37904053 PMCID: PMC10838621 DOI: 10.1038/s41588-023-01537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/18/2023] [Indexed: 11/01/2023]
Abstract
Genetic mutations accumulate in an organism's body throughout its lifetime. While somatic single-nucleotide variants have been well characterized in the human body, the patterns and consequences of large chromosomal alterations in normal tissues remain largely unknown. Here, we present a pan-tissue survey of mosaic chromosomal alterations (mCAs) in 948 healthy individuals from the Genotype-Tissue Expression project, augmenting RNA-based allelic imbalance estimation with haplotype phasing. We found that approximately a quarter of the individuals carry a clonally-expanded mCA in at least one tissue, with incidence strongly correlated with age. The prevalence and genome-wide patterns of mCAs vary considerably across tissue types, suggesting tissue-specific mutagenic exposure and selection pressures. The mCA landscapes in normal adrenal and pituitary glands resemble those in tumors arising from these tissues, whereas the same is not true for the esophagus and skin. Together, our findings show a widespread age-dependent emergence of mCAs across normal human tissues with intricate connections to tumorigenesis.
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Affiliation(s)
- Teng Gao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Maria Eleni Kastriti
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andreas Heinzel
- Department of Nephrology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Arthur S Tischler
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Rainer Oberbauer
- Department of Nephrology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA.
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Heinrich F, Mertz KD, Glatzel M, Beer M, Krasemann S. Using autopsies to dissect COVID-19 pathogenesis. Nat Microbiol 2023; 8:1986-1994. [PMID: 37798476 DOI: 10.1038/s41564-023-01488-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 09/04/2023] [Indexed: 10/07/2023]
Abstract
The emergence of SARS-CoV-2 has resulted in millions of deaths as a result of COVID-19. Suitable models were missing at the beginning of the pandemic, and studies investigating disease pathogenesis relied on patients who had succumbed to COVID-19. Since then, autopsies of patients have substantially contributed to our understanding of the pathogenesis of COVID-19 and associated major organ complications. Here we summarize how autopsies have complemented experimental studies, mainly in animal models, and how they have facilitated critical knowledge of COVID-19 to improve daily clinical practice and develop therapeutic interventions. Employing advanced histopathologic and molecular genetic methods in post-mortem tissues, the COVID-19 pandemic has highlighted the importance of autopsies for virology research and clinical practice in current and emerging infectious diseases.
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Affiliation(s)
- Fabian Heinrich
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten D Mertz
- Institute of Pathology, Kantonsspital Baselland, Liestal, Switzerland
- University of Basel, Basel, Switzerland
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Niskanen JE, Ohlsson Å, Ljungvall I, Drögemüller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petrič AD, Salonen M, Hundi S, Hörtenhuber M, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hytönen MK, Häggström J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H. Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human. Genome Med 2023; 15:73. [PMID: 37723491 PMCID: PMC10506233 DOI: 10.1186/s13073-023-01221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis. METHODS We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts. RESULTS Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes. CONCLUSIONS Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.
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Affiliation(s)
- Julia E Niskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Robert F Ernst
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dennis Dooijes
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hanneke W M van Deutekom
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - J Peter van Tintelen
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Christian J B Snijders Blok
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Marion van Vugt
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | | | - Milla Salonen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Research Programs Unit, Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - W Glen Pyle
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
- IMPART Investigator Team Canada, Dalhousie Medicine, Saint John, NB, Canada
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Helsinki, Finland
| | - Alex V Postma
- Department of Human Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Wiberg
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Jana Friederich
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Jenny Eberhard
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Frank G van Steenbeek
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 108, Utrecht, 3584 CM, The Netherlands
| | - Gerhard Wess
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland.
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland.
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Chu M, Ji H, Li K, Liu H, Peng M, Wang Z, Zhu X. Investigating the potential mechanism of quercetin against cervical cancer. Discov Oncol 2023; 14:170. [PMID: 37704909 PMCID: PMC10499770 DOI: 10.1007/s12672-023-00788-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Cervical cancer is emerging as a potential target of increased susceptibility to coronavirus disease-2019 (COVID-19), leading to compromised survival rates. Despite this critical link, efficacious anti-cervical cancer/COVID-19 interventions remain limited. Quercetin, known for its efficacy against both cancer and viral infections, holds promise as a therapeutic agent. This study aims to elucidate quercetin's anti-cervical cancer/COVID-19 mechanisms and potential targets. METHODS We initiated our investigation with differential gene expression analysis using cervical cancer transcriptome data from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx), focusing on intersections with COVID-19-related genes. Network pharmacology was employed to identify the shared targets between cervical cancer/COVID-19 DEGs and quercetin's targets. Subsequently, Cox proportional hazards analyses were employed to establish a risk score based on these genes. Molecular docking techniques were applied to predict quercetin's therapeutic targets and mechanisms for mitigating cervical cancer and COVID-19. RESULTS Our findings unveiled 45 potential quercetin targets with anti-cervical cancer/COVID-19 actions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted significant enrichment in immune pathways and COVID-19-related pathways. A refined risk score model, comprising PLA2G7, TNF, TYK2, F2, and NRP1, effectively stratified cervical cancer patients into distinct risk groups. Importantly, molecular docking analyses illuminated quercetin's remarkable binding affinity to the primary protease of the coronavirus. CONCLUSIONS In summation, our study suggests that quercetin holds promise as a potential therapeutic agent for mitigating coronavirus function, specifically through its interaction with the primary protease. This research offers novel insights into exploring COVID-19 susceptibility and enhancing survival in cervical cancer patients.
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Affiliation(s)
- Man Chu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Huihui Ji
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Kehan Li
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hejing Liu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Mengjia Peng
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhiwei Wang
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Xueqiong Zhu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China.
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Mannan R, Wang X, Bawa PS, Zhang Y, Skala SL, Chinnaiyan AK, Dagar A, Wang L, Zelenka-Wang SB, McMurry LM, Daniel N, Cao X, Sangoi AR, Gupta S, Vaishampayan UN, Hafez KS, Morgan TM, Spratt DE, Tretiakova MS, Argani P, Chinnaiyan AM, Dhanasekaran SM, Mehra R. Characterization of Intercalated Cell Markers KIT and LINC01187 in Chromophobe Renal Cell Carcinoma and Other Renal Neoplasms. Int J Surg Pathol 2023; 31:1027-1040. [PMID: 36250542 DOI: 10.1177/10668969221125793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Introduction. Chromophobe renal cell carcinoma (chromophobe RCC) is the third major subcategory of renal tumors after clear cell RCC and papillary RCC, accounting for approximately 5% of all RCC subtypes. Other oncocytic neoplasms seen commonly in surgical pathology practice include the eosinophilic variant of chromophobe RCC, renal oncocytoma, and low-grade oncocytic unclassified RCC. Methods. In our recent next-generation sequencing based study, we nominated a lineage-specific novel biomarker LINC01187 (long intergenic non-protein coding RNA 1187) which was found to be enriched in chromophobe RCC. Like KIT (cluster of differentiation 117; CD117), a clinically utilized chromophobe RCC related biomarker, LINC01187 is expressed in intercalated cells of the nephron. In this follow-up study, we performed KIT immunohistochemistry and LINC01187 RNA in situ hybridization (RNA-ISH) on a cohort of chromophobe RCC and other renal neoplasms, characterized the expression patterns, and quantified the expression signals of the two biomarkers in both primary and metastatic settings. Results. LINC01187, in comparison to KIT, exhibits stronger and more uniform expression within tumors while maintaining temporal and spatial consistency. LINC01187 also is devoid of intra-tumoral heterogeneous expression pattern, a phenomenon commonly noted with KIT. Conclusions. LINC01187 expression can augment the currently utilized KIT assay and help facilitate easy microscopic analyses in routine surgical pathology practice.
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Affiliation(s)
- Rahul Mannan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Xiaoming Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Pushpinder S Bawa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Stephanie L Skala
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Aniket Dagar
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Sylvia B Zelenka-Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Lisa M McMurry
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Nikita Daniel
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Xuhong Cao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Ann Arbor, MI, USA
| | - Ankur R Sangoi
- Department of Pathology, El Camino Hospital, Mountain View, CA, USA
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ulka N Vaishampayan
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Khaled S Hafez
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Maria S Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pedram Argani
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
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Chen H, Ma R, Zhou B, Yang X, Duan F, Wang G. Integrated immunological analysis of single-cell and bulky tissue transcriptomes reveals the role of interactions between M0 macrophages and naïve CD4 + T cells in the immunosuppressive microenvironment of cervical cancer. Comput Biol Med 2023; 163:107151. [PMID: 37348264 DOI: 10.1016/j.compbiomed.2023.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/27/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
In recent decades, the incidence and mortality of cervical cancer have declined in developed countries due to the implementation of screening and vaccination programs. However, cervical cancer remains one of the major culprits of cancer-related deaths in young women. Current studies have found that immune cell-related intercellular communication in the tumor microenvironment has a large impact on the construction of the immunosuppressive microenvironment. In this study, we performed a comprehensive immune analysis on bulk RNA-seq and scRNA-seq data obtained from cervical cancer and revealed that two highly plastic cell populations, M0 macrophages and naïve CD4+ T cells, were significantly correlated with prognosis and clinical phenotypes. Notably, signaling between M0 macrophages and naïve CD4+ T cells as well as intracellular transcription factor activity were significantly altered in the tumor state. Furthermore, we identified overlapping genes between the transcription factor target genes of M0 macrophages or naïve CD4+ T cells and the differentially expressed genes in each type of cell, and these overlapping genes were subsequently subjected to an analysis using the LASSO regression model. Finally, we generated a score index that was significantly associated with the clinical prognosis of cervical cancer. In conclusion, interventions to improve the communication between M0 macrophages and naïve CD4+ T cells may help to improve the immunosuppressive microenvironment of cervical cancer and prevent immune evasion. The relevant molecular mechanisms need to be further validated by experimental and cohort studies.
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Affiliation(s)
- Huaqiu Chen
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China; Department of Laboratory, Xichang People's Hospital, Sichuan, 615000, China
| | - Rong Ma
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China; Department of Laboratory, The First People's Hospital of Qujing, Yunnan Province, 655000, China
| | - Bingjie Zhou
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China; Maternity and Obstetrics Department of Fangshan District Maternity and Child Health Hospital of Beijing, Fangshan District of Beijing, 102488, China
| | - Xitong Yang
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China
| | - Fuhui Duan
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China
| | - Guangming Wang
- Center of Genetic Testing, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, 671000, China.
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Fass SB, Mulvey B, Yang W, Selmanovic D, Chaturvedi S, Tycksen E, Weiss LA, Dougherty JD. Relationship between sex biases in gene expression and sex biases in autism and Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.29.23294773. [PMID: 37693465 PMCID: PMC10491382 DOI: 10.1101/2023.08.29.23294773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Sex differences in the brain may play an important role in sex-differential prevalence of neuropsychiatric conditions. In order to understand the transcriptional basis of sex differences, we analyzed multiple, large-scale, human postmortem brain RNA-seq datasets using both within-region and pan-regional frameworks. We find evidence of sex-biased transcription in many autosomal genes, some of which provide evidence for pathways and cell population differences between chromosomally male and female individuals. These analyses also highlight regional differences in the extent of sex-differential gene expression. We observe an increase in specific neuronal transcripts in male brains and an increase in immune and glial function-related transcripts in female brains. Integration with single-cell data suggests this corresponds to sex differences in cellular states rather than cell abundance. Integration with case-control gene expression studies suggests a female molecular predisposition towards Alzheimer's disease, a female-biased disease. Autism, a male-biased diagnosis, does not exhibit a male predisposition pattern in our analysis. Finally, we provide region specific analyses of sex differences in brain gene expression to enable additional studies at the interface of gene expression and diagnostic differences.
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Affiliation(s)
- Stuart B Fass
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
| | - Bernard Mulvey
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- Lieber Institute for Brain Development, 855 North Wolfe St. Ste 300, Baltimore, MD 21205, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Din Selmanovic
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
| | - Sneha Chaturvedi
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
| | - Eric Tycksen
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lauren A Weiss
- Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Ave, HSE901, San Francisco, CA 94143
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, 513 Parnassus Ave, HSE901, San Francisco, CA 94143
- Weill Institute for Neurosciences, University of California, San Francisco, 513 Parnassus Ave, HSE901, San Francisco, CA 94143
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63110, USA
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Salihefendić L, Čeko I, Bešić L, Mulahuseinović N, Durgut S, Pećar D, Prnjavorac L, Kandić E, Meseldžić N, Bego T, Prnjavorac B, Marjanović D, Konjhodžić R, Ašić A. Identification of human genetic variants modulating the course of COVID-19 infection with importance in other viral infections. Front Genet 2023; 14:1240245. [PMID: 37795240 PMCID: PMC10545899 DOI: 10.3389/fgene.2023.1240245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/11/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction: COVID-19 has been a major focus of scientific research since early 2020. Due to its societal, economic, and clinical impact worldwide, research efforts aimed, among other questions, to address the effect of host genetics in susceptibility and severity of COVID-19. Methods: We, therefore, performed next-generation sequencing of coding and regulatory regions of 16 human genes, involved in maintenance of the immune system or encoding receptors for viral entry into the host cells, in a subset of 60 COVID-19 patients from the General Hospital Tešanj, Bosnia and Herzegovina, classified into three groups of clinical conditions of different severity ("mild," "moderate," and "severe"). Results: We confirmed that the male sex and older age are risk factors for severe clinical picture and identified 13 variants on seven genes (CD55, IL1B, IL4, IRF7, DDX58, TMPRSS2, and ACE2) with potential functional significance, either as genetic markers of modulated susceptibility to SARS-CoV-2 infection or modifiers of the infection severity. Our results include variants reported for the first time as potentially associated with COVID-19, but further research and larger patient cohorts are required to confirm their effect. Discussion: Such studies, focused on candidate genes and/or variants, have a potential to answer the questions regarding the effect of human genetic makeup on the expected infection outcome. In addition, loci we identified here were previously reported to have clinical significance in other diseases and viral infections, thus confirming a general, broader significance of COVID-19-related research results following the end of the pandemic period.
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Affiliation(s)
- Lana Salihefendić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Ivana Čeko
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | | | - Selma Durgut
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | - Dino Pećar
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | | | - Enis Kandić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | - Neven Meseldžić
- Department of Pharmaceutical Biochemistry and Laboratory Diagnostics, Faculty of Pharmacy, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Tamer Bego
- Department of Pharmaceutical Biochemistry and Laboratory Diagnostics, Faculty of Pharmacy, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Damir Marjanović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
- Institute for Anthropological Research, University of Zagreb, Zagreb, Croatia
| | - Rijad Konjhodžić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Adna Ašić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
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