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Aumailley L, Bodein A, Adjibade P, Leclercq M, Bourassa S, Droit A, Mazroui R, Lebel M. Combined transcriptomics and proteomics unveil the impact of vitamin C in modulating specific protein abundance in the mouse liver. Biol Res 2024; 57:26. [PMID: 38735981 PMCID: PMC11088995 DOI: 10.1186/s40659-024-00509-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: 11/24/2023] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Vitamin C (ascorbate) is a water-soluble antioxidant and an important cofactor for various biosynthetic and regulatory enzymes. Mice can synthesize vitamin C thanks to the key enzyme gulonolactone oxidase (Gulo) unlike humans. In the current investigation, we used Gulo-/- mice, which cannot synthesize their own ascorbate to determine the impact of this vitamin on both the transcriptomics and proteomics profiles in the whole liver. The study included Gulo-/- mouse groups treated with either sub-optimal or optimal ascorbate concentrations in drinking water. Liver tissues of females and males were collected at the age of four months and divided for transcriptomics and proteomics analysis. Immunoblotting, quantitative RT-PCR, and polysome profiling experiments were also conducted to complement our combined omics studies. RESULTS Principal component analyses revealed distinctive differences in the mRNA and protein profiles as a function of sex between all the mouse cohorts. Despite such sexual dimorphism, Spearman analyses of transcriptomics data from females and males revealed correlations of hepatic ascorbate levels with transcripts encoding a wide array of biological processes involved in glucose and lipid metabolisms as well as in the acute-phase immune response. Moreover, integration of the proteomics data showed that ascorbate modulates the abundance of various enzymes involved in lipid, xenobiotic, organic acid, acetyl-CoA, and steroid metabolism mainly at the transcriptional level, especially in females. However, several proteins of the mitochondrial complex III significantly correlated with ascorbate concentrations in both males and females unlike their corresponding transcripts. Finally, poly(ribo)some profiling did not reveal significant enrichment difference for these mitochondrial complex III mRNAs between Gulo-/- mice treated with sub-optimal and optimal ascorbate levels. CONCLUSIONS Thus, the abundance of several subunits of the mitochondrial complex III are regulated by ascorbate at the post-transcriptional levels. Our extensive omics analyses provide a novel resource of altered gene expression patterns at the transcriptional and post-transcriptional levels under ascorbate deficiency.
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Affiliation(s)
- Lucie Aumailley
- Centre de recherche du CHU de Québec, Faculty of Medicine, Université Laval, 2705 Laurier Blvd., Local R-2714, Québec City, QC, G1V 4G2, Canada
| | - Antoine Bodein
- Endocrinology and Nephrology Unit, CHU de Québec-Laval University Research Center, Québec City, QC, Canada
| | - Pauline Adjibade
- Cancer Research Center, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Mickaël Leclercq
- Endocrinology and Nephrology Unit, CHU de Québec-Laval University Research Center, Québec City, QC, Canada
| | - Sylvie Bourassa
- Proteomics Platform, Centre de recherche du CHU de Québec, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 4G2, Canada
| | - Arnaud Droit
- Endocrinology and Nephrology Unit, CHU de Québec-Laval University Research Center, Québec City, QC, Canada
- Proteomics Platform, Centre de recherche du CHU de Québec, Faculty of Medicine, Université Laval, Quebec City, QC, G1V 4G2, Canada
| | - Rachid Mazroui
- Cancer Research Center, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Michel Lebel
- Centre de recherche du CHU de Québec, Faculty of Medicine, Université Laval, 2705 Laurier Blvd., Local R-2714, Québec City, QC, G1V 4G2, Canada.
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Robinson K, Parrish R, Adeyemo WL, Beaty TH, Butali A, Buxó CJ, Gowans LJ, Hecht JT, Moreno L, Murray JC, Shaw GM, Weinberg SM, Brand H, Marazita ML, Cutler DJ, Epstein MP, Yang J, Leslie EJ. Genome-wide study of gene-by-sex interactions identifies risks for cleft palate. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306701. [PMID: 38746184 PMCID: PMC11092717 DOI: 10.1101/2024.05.01.24306701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Structural birth defects affect 3-4% of all live births and, depending on the type, tend to manifest in a sex-biased manner. Orofacial clefts (OFCs) are the most common craniofacial structural birth defects and are often divided into cleft lip with or without cleft palate (CL/P) and cleft palate only (CP). Previous studies have found sex-specific risks for CL/P, but these risks have yet to be evaluated in CP. CL/P is more common in males and CP is more frequently observed in females, so we hypothesized there would also be sex-specific differences for CP. Using a trio-based cohort, we performed sex-stratified genome-wide association studies (GWAS) based on proband sex followed by a genome-wide gene-by-sex (GxS) interaction testing. There were 13 loci significant for GxS interactions, with the top finding in LTBP1 (RR=3.37 [2.04 - 5.56], p=1.93x10 -6 ). LTBP1 plays a role in regulating TGF-B bioavailability, and knockdown in both mice and zebrafish lead to craniofacial anomalies. Further, there is evidence for differential expression of LTBP1 between males and females in both mice and humans. Therefore, we tested the association between the imputed genetically regulated gene expression of genes with significant GxS interactions and the CP phenotype. We found significant association for LTBP1 in cell cultured fibroblasts in female probands (p=0.0013) but not in males. Taken altogether, we show there are sex-specific risks for CP that are otherwise undetectable in a combined sex cohort, and LTBP1 is a candidate risk gene, particularly in females.
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Drouard G, Hagenbeek FA, Whipp AM, Pool R, Hottenga JJ, Jansen R, Hubers N, Afonin A, Willemsen G, de Geus EJC, Ripatti S, Pirinen M, Kanninen KM, Boomsma DI, van Dongen J, Kaprio J. Longitudinal multi-omics study reveals common etiology underlying association between plasma proteome and BMI trajectories in adolescent and young adult twins. BMC Med 2023; 21:508. [PMID: 38129841 PMCID: PMC10740308 DOI: 10.1186/s12916-023-03198-7] [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: 07/03/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND The influence of genetics and environment on the association of the plasma proteome with body mass index (BMI) and changes in BMI remains underexplored, and the links to other omics in these associations remain to be investigated. We characterized protein-BMI trajectory associations in adolescents and adults and how these connect to other omics layers. METHODS Our study included two cohorts of longitudinally followed twins: FinnTwin12 (N = 651) and the Netherlands Twin Register (NTR) (N = 665). Follow-up comprised 4 BMI measurements over approximately 6 (NTR: 23-27 years old) to 10 years (FinnTwin12: 12-22 years old), with omics data collected at the last BMI measurement. BMI changes were calculated in latent growth curve models. Mixed-effects models were used to quantify the associations between the abundance of 439 plasma proteins with BMI at blood sampling and changes in BMI. In FinnTwin12, the sources of genetic and environmental variation underlying the protein abundances were quantified by twin models, as were the associations of proteins with BMI and BMI changes. In NTR, we investigated the association of gene expression of genes encoding proteins identified in FinnTwin12 with BMI and changes in BMI. We linked identified proteins and their coding genes to plasma metabolites and polygenic risk scores (PRS) applying mixed-effects models and correlation networks. RESULTS We identified 66 and 14 proteins associated with BMI at blood sampling and changes in BMI, respectively. The average heritability of these proteins was 35%. Of the 66 BMI-protein associations, 43 and 12 showed genetic and environmental correlations, respectively, including 8 proteins showing both. Similarly, we observed 7 and 3 genetic and environmental correlations between changes in BMI and protein abundance, respectively. S100A8 gene expression was associated with BMI at blood sampling, and the PRG4 and CFI genes were associated with BMI changes. Proteins showed strong connections with metabolites and PRSs, but we observed no multi-omics connections among gene expression and other omics layers. CONCLUSIONS Associations between the proteome and BMI trajectories are characterized by shared genetic, environmental, and metabolic etiologies. We observed few gene-protein pairs associated with BMI or changes in BMI at the proteome and transcriptome levels.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Fiona A Hagenbeek
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Alyce M Whipp
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Rick Jansen
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, The Netherlands
| | - Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Aleksei Afonin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Katja M Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
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4
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Kosmara D, Papanikolaou S, Nikolaou C, Bertsias G. Extensive Alternative Splicing Patterns in Systemic Lupus Erythematosus Highlight Sexual Differences. Cells 2023; 12:2678. [PMID: 38067106 PMCID: PMC10705143 DOI: 10.3390/cells12232678] [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: 10/13/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Substantial evidence highlights divergences in immune responses between men and women. Women are more susceptible to autoimmunity, whereas men suffer from the more severe presentation of autoimmune disorders. The molecular mechanism of this sexual dimorphism remains elusive. Herein, we conducted a comprehensive analysis of sex differences in whole-blood gene expression focusing on alternative splicing (AS) events in systemic lupus erythematosus (SLE), which is a prototype sex-biased disease. This study included 79 SLE patients with active disease and 58 matched healthy controls who underwent whole-blood RNA sequencing. Sex differences in splicing events were widespread, existent in both SLE and a healthy state. However, we observed distinct gene sets and molecular pathways targeted by sex-dependent AS in SLE patients as compared to healthy subjects, as well as a notable sex dissimilarity in intron retention events. Sexually differential spliced genes specific to SLE patients were enriched for dynamic cellular processes including chromatin remodeling, stress and inflammatory responses. Remarkably, the extent of sexual differences in AS in the SLE patients and healthy individuals exceeded those in gene expression. Overall, this study reveals an unprecedent variation in sex-dependent splicing events in SLE and the healthy state, with potential implications for understanding the molecular basis of sexual dimorphism in autoimmunity.
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Affiliation(s)
- Despoina Kosmara
- Rheumatology and Clinical Immunology, University Hospital of Heraklion and University of Crete Medical School, 71500 Heraklion, Greece
- Foundation for Research and Technology-Hellas (FORTH), Infections and Immunity, Institute of Molecular Biology and Biotechnology, 71110 Heraklion, Greece
| | - Sofia Papanikolaou
- Rheumatology and Clinical Immunology, University Hospital of Heraklion and University of Crete Medical School, 71500 Heraklion, Greece
- Biomedical Sciences Research Center “Alexander Fleming”, Institute of Bioinnovation, 16672 Athens, Greece
| | - Christoforos Nikolaou
- Biomedical Sciences Research Center “Alexander Fleming”, Institute of Bioinnovation, 16672 Athens, Greece
| | - George Bertsias
- Rheumatology and Clinical Immunology, University Hospital of Heraklion and University of Crete Medical School, 71500 Heraklion, Greece
- Foundation for Research and Technology-Hellas (FORTH), Infections and Immunity, Institute of Molecular Biology and Biotechnology, 71110 Heraklion, Greece
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5
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Collins HE. Female cardiovascular biology and resilience in the setting of physiological and pathological stress. Redox Biol 2023; 63:102747. [PMID: 37216702 PMCID: PMC10209889 DOI: 10.1016/j.redox.2023.102747] [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] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
For years, females were thought of as smaller men with complex hormonal cycles; as a result, females have been largely excluded from preclinical and clinical research. However, in the last ten years, with the increased focus on sex as a biological variable, it has become clear that this is not the case, and in fact, male and female cardiovascular biology and cardiac stress responses differ substantially. Premenopausal women are protected from cardiovascular diseases, such as myocardial infarction and resultant heart failure, having preserved cardiac function, reduced adverse remodeling, and increased survival. Many underlying biological processes that contribute to ventricular remodeling differ between the sexes, such as cellular metabolism; immune cell responses; cardiac fibrosis and extracellular matrix remodeling; cardiomyocyte dysfunction; and endothelial biology; however, it is unclear how these changes afford protection to the female heart. Although many of these changes are dependent on protection provided by female sex hormones, several of these changes occur independent of sex hormones, suggesting that the nature of these changes is more complex than initially thought. This may be why studies focused on the cardiovascular benefits of hormone replacement therapy in post-menopausal women have provided mixed results. Some of the complexity likely stems from the fact that the cellular composition of the heart is sexually dimorphic and that in the setting of MI, different subpopulations of these cell types are apparent. Despite the documented sex-differences in cardiovascular (patho)physiology, the underlying mechanisms that contribute are largely unknown due to inconsistent findings amongst investigators and, in some cases, lack of rigor in reporting and consideration of sex-dependent variables. Therefore, this review aims to describe current understanding of the sex-dependent differences in the myocardium in response to physiological and pathological stressors, with a focus on the sex-dependent differences that contribute to post-infarction remodeling and resultant functional decline.
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Affiliation(s)
- Helen E Collins
- Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, Division of Environmental Medicine, Department of Medicine, Delia B. Baxter Research Building, University of Louisville, 580 S. Preston S, Louisville, KY 40202, USA.
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6
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Drouard G, Hagenbeek FA, Whipp A, Pool R, Hottenga JJ, Jansen R, Hubers N, Afonin A, Willemsen G, de Geus EJC, Ripatti S, Pirinen M, Kanninen KM, Boomsma DI, van Dongen J, Kaprio J. Longitudinal multi-omics study reveals common etiology underlying association between plasma proteome and BMI trajectories in adolescent and young adult twins. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.28.23291995. [PMID: 37425750 PMCID: PMC10327285 DOI: 10.1101/2023.06.28.23291995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Background The influence of genetics and environment on the association of the plasma proteome with body mass index (BMI) and changes in BMI remain underexplored, and the links to other omics in these associations remain to be investigated. We characterized protein-BMI trajectory associations in adolescents and adults and how these connect to other omics layers. Methods Our study included two cohorts of longitudinally followed twins: FinnTwin12 (N=651) and the Netherlands Twin Register (NTR) (N=665). Follow-up comprised four BMI measurements over approximately 6 (NTR: 23-27 years old) to 10 years (FinnTwin12: 12-22 years old), with omics data collected at the last BMI measurement. BMI changes were calculated using latent growth curve models. Mixed-effects models were used to quantify the associations between the abundance of 439 plasma proteins with BMI at blood sampling and changes in BMI. The sources of genetic and environmental variation underlying the protein abundances were quantified using twin models, as were the associations of proteins with BMI and BMI changes. In NTR, we investigated the association of gene expression of genes encoding proteins identified in FinnTwin12 with BMI and changes in BMI. We linked identified proteins and their coding genes to plasma metabolites and polygenic risk scores (PRS) using mixed-effect models and correlation networks. Results We identified 66 and 14 proteins associated with BMI at blood sampling and changes in BMI, respectively. The average heritability of these proteins was 35%. Of the 66 BMI-protein associations, 43 and 12 showed genetic and environmental correlations, respectively, including 8 proteins showing both. Similarly, we observed 6 and 4 genetic and environmental correlations between changes in BMI and protein abundance, respectively. S100A8 gene expression was associated with BMI at blood sampling, and the PRG4 and CFI genes were associated with BMI changes. Proteins showed strong connections with many metabolites and PRSs, but we observed no multi-omics connections among gene expression and other omics layers. Conclusions Associations between the proteome and BMI trajectories are characterized by shared genetic, environmental, and metabolic etiologies. We observed few gene-protein pairs associated with BMI or changes in BMI at the proteome and transcriptome levels.
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Affiliation(s)
- Gabin Drouard
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Fiona A. Hagenbeek
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Alyce Whipp
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Rick Jansen
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Psychiatry, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, The Netherlands
| | - Nikki Hubers
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Aleksei Afonin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - BIOS Consortium
- Biobank-based Integrative Omics Study Consortium. Lists of authors and their affiliations appear in the supplementary material (see Additional file 1)
| | | | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Eco J. C. de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Katja M. Kanninen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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7
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Tran NQV, Le MK, Nguyen TA, Kondo T, Nakao A. Association of Circadian Clock Gene Expression with Pediatric/Adolescent Asthma and Its Comorbidities. Int J Mol Sci 2023; 24:ijms24087477. [PMID: 37108640 PMCID: PMC10138904 DOI: 10.3390/ijms24087477] [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: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The pathology of asthma is characterized by marked day-night variation, which is likely controlled by circadian clock activity. This study aimed to clarify the association of core circadian clock gene expression with clinical features of asthma. For this purpose, we accessed the National Center for Biotechnology Information database and analyzed transcriptomes of peripheral blood mononuclear cells and clinical characteristics of 134 pediatric/adolescent patients with asthma. Based on the expression patterns of seven core circadian clock genes (CLOCK, BMAL1, PER1-3, CRY1-2), we identified three circadian clusters (CCs) with distinct comorbidities and transcriptomic expressions. In the three CC subtypes, allergic rhinitis, and atopic dermatitis, both asthma comorbidities occurred in different proportions: CC1 had a high proportion of allergic rhinitis and atopic dermatitis; CC2 had a high proportion of atopic dermatitis but a low proportion of allergic rhinitis; and CC3 had a high proportion of allergic rhinitis but a low proportion of atopic dermatitis. This might be associated with the low activity of the FcεRI signaling pathway in CC2 and the cytokine-cytokine receptor interaction pathways in CC3. This is the first report to consider circadian clock gene expression in subcategories of patients with asthma and to explore their contribution to pathophysiology and comorbidity.
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Affiliation(s)
- Nguyen Quoc Vuong Tran
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Minh-Khang Le
- Department of Human Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Thuy-An Nguyen
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Tetsuo Kondo
- Department of Human Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Atsuhito Nakao
- Department of Immunology, Faculty of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
- Atopy Research Center, Juntendo University, School of Medicine, Tokyo 113-8421, Japan
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8
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Genetics and epigenetics of primary Sjögren syndrome: implications for future therapies. Nat Rev Rheumatol 2023; 19:288-306. [PMID: 36914790 PMCID: PMC10010657 DOI: 10.1038/s41584-023-00932-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/14/2023]
Abstract
In primary Sjögren syndrome (pSS), chronic inflammation of exocrine glands results in tissue destruction and sicca symptoms, primarily of the mouth and eyes. Fatigue, arthralgia and myalgia are also common symptoms, whereas extraglandular manifestations that involve the respiratory, nervous and vascular systems occur in a subset of patients. The disease predominantly affects women, with an estimated female to male ratio of 14 to 1. The aetiology of pSS, however, remains incompletely understood, and effective treatment is lacking. Large-scale genetic and epigenetic investigations have revealed associations between pSS and genes in both innate and adaptive immune pathways. The genetic variants mediate context-dependent effects, and both sex and environmental factors can influence the outcome. As such, genetic and epigenetic studies can provide insight into the dysregulated molecular mechanisms, which in turn might reveal new therapeutic possibilities. This Review discusses the genetic and epigenetic features that have been robustly connected with pSS, putting them into the context of cellular function, carrier sex and environmental challenges. In all, the observations point to several novel opportunities for early detection, treatment development and the pathway towards personalized medicine.
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9
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Suarez LM, Diaz-Del Cerro E, Felix J, Gonzalez-Sanchez M, Ceprian N, Guerra-Perez N, G Novelle M, Martinez de Toda I, De la Fuente M. Sex differences in neuroimmunoendocrine communication. Involvement on longevity. Mech Ageing Dev 2023; 211:111798. [PMID: 36907251 DOI: 10.1016/j.mad.2023.111798] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Endocrine, nervous, and immune systems work coordinately to maintain the global homeostasis of the organism. They show sex differences in their functions that, in turn, contribute to sex differences beyond reproductive function. Females display a better control of the energetic metabolism and improved neuroprotection and have more antioxidant defenses and a better inflammatory status than males, which is associated with a more robust immune response than that of males. These differences are present from the early stages of life, being more relevant in adulthood and influencing the aging trajectory in each sex and may contribute to the different life lifespan between sexes.
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Affiliation(s)
- Luz M Suarez
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain.
| | - Estefania Diaz-Del Cerro
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Judith Felix
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Monica Gonzalez-Sanchez
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Noemi Ceprian
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Natalia Guerra-Perez
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Marta G Novelle
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain
| | - Irene Martinez de Toda
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Monica De la Fuente
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain.
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10
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García-Pérez R, Ramirez JM, Ripoll-Cladellas A, Chazarra-Gil R, Oliveros W, Soldatkina O, Bosio M, Rognon PJ, Capella-Gutierrez S, Calvo M, Reverter F, Guigó R, Aguet F, Ferreira PG, Ardlie KG, Melé M. The landscape of expression and alternative splicing variation across human traits. CELL GENOMICS 2022; 3:100244. [PMID: 36777183 PMCID: PMC9903719 DOI: 10.1016/j.xgen.2022.100244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.
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Affiliation(s)
- Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Jose Miguel Ramirez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Aida Ripoll-Cladellas
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Ruben Chazarra-Gil
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Winona Oliveros
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Oleksandra Soldatkina
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Mattia Bosio
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Paul Joris Rognon
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Catalonia 08005, Spain,Department of Statistics and Operations Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia 08034, Spain
| | - Salvador Capella-Gutierrez
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain
| | - Miquel Calvo
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Ferran Reverter
- Statistics Section, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Catalonia 08028, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalonia 08003, Spain
| | | | - Pedro G. Ferreira
- Department of Computer Science, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal,Laboratory of Artificial Intelligence and Decision Support, INESC TEC, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,Institute of Molecular Pathology and Immunology of the University of Porto, Institute for Research and Innovation in Health (i3s), R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | | | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Center (BCN-CNS), Barcelona, Catalonia 08034, Spain,Corresponding author
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11
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Kim H, Choo H, Cha J, Jang M, Son J, Jeong T, Choi BH, Lim Y, Chai HH, Lee J, Lim D, Shin D, Park W, Park JE. Blood transcriptome comparison between sexes and their function in 4-week Rhode Island red chickens. Anim Cells Syst (Seoul) 2022; 26:358-368. [PMID: 36605592 PMCID: PMC9809412 DOI: 10.1080/19768354.2022.2146187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sex is a major biological factor in the development and physiology of a sexual reproductive organism, and its role in the growing process is needed to be investigated in various species. We compare blood transcriptome between 5 males and 5 females in 4-week-old Rhode Island Red chickens and perform functional annotation of differentially expressed genes (DEGs). The results are as follows. 141 and 109 DEGs were located in autosomes and sex chromosomes, respectively. The gene ontology (GO) terms are significantly (p < 0.05) enriched, which were limb development, inner ear development, positive regulation of dendrite development, the KEGG pathway the TGF-beta signaling pathway, and melanogenesis (p < 0.05). These pathways are related to morphological maintenance and growth of the tissues. In addition, the SMAD2W and the BMP5 were involved in the TGF-beta signaling pathway, and both play an important role in maintaining tissue development. The major DEGs related to the development of neurons and synapses include the up-regulated NRN1, GDF10, SLC1A1, BMP5, NBEA, and NRXN1. Also, 7 DEGs were validated using RT-qPCR with high correlation (r 2 = 0.74). In conclusion, the differential expression of blood tissue in the early growing chicken was enriched in TGF-beta signaling and related to the development of neurons and synapses including SMAD2W and BMP5. These results suggest that blood in the early growing stage is differentially affected in tissue development, nervous system, and pigmentation by sex. For future research, experimental characterization of DEGs and a holistic investigation of various tissues and growth stages will be required.
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Affiliation(s)
- Hana Kim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Hyojun Choo
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang, Korea
| | - Jihye Cha
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Myoungjin Jang
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Juhwan Son
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Taejoon Jeong
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Bong-Hwan Choi
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Youngjo Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Han-Ha Chai
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, Korea
| | - Dajeong Lim
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Korea
| | - Woncheoul Park
- Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, Korea, Jong-Eun Park Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju-si, 63243, Korea; Woncheoul Park Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Wanju, 55365, Korea
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12
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Coales I, Tsartsalis S, Fancy N, Weinert M, Clode D, Owen D, Matthews PM. Alzheimer's disease-related transcriptional sex differences in myeloid cells. J Neuroinflammation 2022; 19:247. [PMID: 36199077 PMCID: PMC9535846 DOI: 10.1186/s12974-022-02604-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022] Open
Abstract
Sex differences have been identified in many diseases associated with dysregulated immune responses, including Alzheimer's disease (AD), for which approximately two-thirds of patients are women. An accumulating body of research indicates that microglia may play a causal role in the pathogenesis of this disease. We hypothesised that sex differences in the transcriptome of human myeloid cells may contribute to the sex difference observed in AD prevalence. To explore this, we assessed bulk and single-nuclear RNA sequencing data sets generated from four human derived myeloid cell populations: post-mortem microglial nuclei, peripheral monocytes, monocyte-derived macrophages (MDMs) and induced pluripotent stem cell derived microglial-like cells (MGLs). We found that expression of AD risk genes, gene signatures associated with the inflammatory response in AD, and genes related to proinflammatory immune responses were enriched in microglial nuclei isolated from aged female donors without ante-mortem neurological disease, relative to those from males. In addition, these inflammation-associated gene sets were found to be enriched in peripheral monocytes isolated from postmenopausal women and in MDMs obtained from premenopausal individuals relative to age-matched males. Expression of these gene sets did not differ in MDMs derived from women whose blood was sampled across the menstrual cycle or in MGLs cultured with 17β-oestradiol. This suggests that the observed gene set enrichments in myeloid cells from women were not being driven by acute hormonal influences. Together, these data support the hypothesis that the increased prevalence of AD in women may be partly explained by a myeloid cell phenotype biased towards expression of biological processes relevant to AD.
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Affiliation(s)
- Isabelle Coales
- Department of Brain Sciences, Imperial College London, London, UK
- Centre for Host Microbiome Interactions, King's College London, London, SE1 9RT, UK
| | - Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, London, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Nurun Fancy
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Centre at Imperial College London, London, UK
| | - Maria Weinert
- Department of Brain Sciences, Imperial College London, London, UK
| | - Daniel Clode
- UK Dementia Research Centre at Imperial College London, London, UK
| | - David Owen
- Department of Brain Sciences, Imperial College London, London, UK.
- Clinical Research Facility, Hammersmith Hospital, ICTM Building, DuCane Road, London, W12 0NN, UK.
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, London, UK.
- UK Dementia Research Centre at Imperial College London, London, UK.
- Hammersmith Hospital, E502, Burlington Danes Building, DuCane Road, London, W12 0NN, UK.
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13
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Vlaanderen J, Vermeulen R, Whitaker M, Chadeau-Hyam M, Hottenga JJ, de Geus E, Willemsen G, Penninx BWJH, Jansen R, Boomsma DI. Impact of long-term exposure to PM 2.5 on peripheral blood gene expression pathways involved in cell signaling and immune response. ENVIRONMENT INTERNATIONAL 2022; 168:107491. [PMID: 36081220 DOI: 10.1016/j.envint.2022.107491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Exposure to ambient air pollution, even at low levels, is a major environmental health risk. The peripheral blood transcriptome provides a potential avenue for the elucidation of ambient air pollution related biological perturbations. We assessed the association between long-term estimates for seven priority air pollutants and perturbations in peripheral blood transcriptomics data collected in the Dutch National Twin Register (NTR) and Netherlands Study of Depression and Anxiety (NESDA) cohorts. METHODS In both the discovery (n = 2438) and replication (n = 1567) cohort, outdoor concentration of 7 air pollutants (NO2, NOx, particulate matter (PM2.5, PM2.5abs, PM10, PMcoarse), and ultrafine particles) was predicted with land use regression models. Gene expression was assessed by Affymetrix U219 arrays. Multi-variable univariate mixed-effect models were applied to test for an association between the air pollutants and the transcriptome. Functional analysis was conducted in DAVID. RESULTS In the discovery cohort, we observed for 335 genes (374 probes with FDR < 5 %) a perturbation in peripheral blood gene expression that was associated with long-term average levels of PM2.5. For 69 genes pooled effect estimates from the NTR and NESDA cohorts were significant. Identified genes play a role in biological pathways related to cell signaling and immune response. Sixty-two out of 69 genes had a similar direction of effect in an analysis in which we regressed the probes on differential PM2.5 exposure within monozygotic twin pairs, indicating that the observed differences in gene expression were likely driven by differences in air pollution, rather than by confounding by genetic factors. CONCLUSION Our results indicate that PM2.5 can elicit a response in cell signaling and the immune system, both hallmarks of environmental diseases. The differential effect that we observed between air pollutants may aid in the understanding of differential health effects that have been observed with these exposures.
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Affiliation(s)
- Jelle Vlaanderen
- Institute for Risk Assessment Sciences, Utrecht University, the Netherlands.
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | | | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Eco de Geus
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Rick Jansen
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
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14
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17β-Oestradiol Protects from Hepatitis C Virus Infection through Induction of Type I Interferon. Viruses 2022; 14:v14081806. [PMID: 36016428 PMCID: PMC9415988 DOI: 10.3390/v14081806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/10/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aims: Sex hormones are widely recognised to act as protective factors against several viral infections. Specifically, females infected by the hepatitis C virus display higher clearance rates and reduced disease progression than those found in males. Through modulation of particle release and spread, 17β-oestradiol controls HCV’s life cycle. We investigated the mechanism(s) behind oestrogen’s antiviral effect. Methods: We used cell culture-derived hepatitis C virus in in vitro assays to evaluate the effect of 17β-oestradiol on the innate immune response. Host immune responses were evaluated by enumerating gene transcripts via RT-qPCR in cells exposed to oestrogen in the presence or absence of viral infection. Antiviral effects were determined by focus-forming unit assay or HCV RNA quantification. Results: Stimulation of 17β-oestradiol triggers a pre-activated antiviral state in hepatocytes, which can be maintained for several hours after the hormone is removed. This induction results in the elevation of several innate immune genes, such as interferon alpha and beta, tumour necrosis factor, toll-like receptor 3 and interferon regulatory factor 5. We demonstrated that this pre-activation of immune response signalling is not affected by a viral presence, and the antiviral state can be ablated using an interferon-alpha/beta receptor alpha inhibitor. Finally, we proved that the oestrogen-induced stimulation is essential to generate an antiviral microenvironment mediated by activation of type I interferons. Conclusion: Resulting in viral control and suppression, 17β-oestradiol induces an interferon-mediated antiviral state in hepatocytes. Oestrogen-stimulated cells modulate the immune response through secretion of type I interferon, which can be countered by blocking interferon-alpha/beta receptor alpha signalling.
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15
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Porcu E, Claringbould A, Weihs A, Lepik K, Richardson TG, Völker U, Santoni FA, Teumer A, Franke L, Reymond A, Kutalik Z. Limited evidence for blood eQTLs in human sexual dimorphism. Genome Med 2022; 14:89. [PMID: 35953856 PMCID: PMC9373355 DOI: 10.1186/s13073-022-01088-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The genetic underpinning of sexual dimorphism is very poorly understood. The prevalence of many diseases differs between men and women, which could be in part caused by sex-specific genetic effects. Nevertheless, only a few published genome-wide association studies (GWAS) were performed separately in each sex. The reported enrichment of expression quantitative trait loci (eQTLs) among GWAS-associated SNPs suggests a potential role of sex-specific eQTLs in the sex-specific genetic mechanism underlying complex traits. METHODS To explore this scenario, we combined sex-specific whole blood RNA-seq eQTL data from 3447 European individuals included in BIOS Consortium and GWAS data from UK Biobank. Next, to test the presence of sex-biased causal effect of gene expression on complex traits, we performed sex-specific transcriptome-wide Mendelian randomization (TWMR) analyses on the two most sexually dimorphic traits, waist-to-hip ratio (WHR) and testosterone levels. Finally, we performed power analysis to calculate the GWAS sample size needed to observe sex-specific trait associations driven by sex-biased eQTLs. RESULTS Among 9 million SNP-gene pairs showing sex-combined associations, we found 18 genes with significant sex-biased cis-eQTLs (FDR 5%). Our phenome-wide association study of the 18 top sex-biased eQTLs on >700 traits unraveled that these eQTLs do not systematically translate into detectable sex-biased trait-associations. In addition, we observed that sex-specific causal effects of gene expression on complex traits are not driven by sex-specific eQTLs. Power analyses using real eQTL- and causal-effect sizes showed that millions of samples would be necessary to observe sex-biased trait associations that are fully driven by sex-biased cis-eQTLs. Compensatory effects may further hamper their detection. CONCLUSIONS Our results suggest that sex-specific eQTLs in whole blood do not translate to detectable sex-specific trait associations of complex diseases, and vice versa that the observed sex-specific trait associations cannot be explained by sex-specific eQTLs.
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Affiliation(s)
- Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Center for Primary Care and Public Health, Lausanne, Switzerland.
| | - Annique Claringbould
- University Medical Centre Groningen, Groningen, the Netherlands.,Structural and Computational Biology Unit, European Molecular Biology Laboratories (EMBL), Heidelberg, Germany
| | - Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Kaido Lepik
- Institute of Computer Science, University of Tartu, Tartu, Estonia.,Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Novo Nordisk Research Centre Oxford, Old Road Campus, Oxford, OX3 7DQ, UK
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Federico A Santoni
- Endocrine, Diabetes, and Metabolism Service, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.,Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alexander Teumer
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.,Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Lude Franke
- University Medical Centre Groningen, Groningen, the Netherlands
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Center for Primary Care and Public Health, Lausanne, Switzerland. .,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
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16
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Abstract
PURPOSE OF REVIEW This review aims to describe how the clinical manifestations of sarcoidosis may be shaped by the effects of sex hormones and by age dependent changes in immune functions and physiology This review is intended to highlight the need to consider the effects of sex and sex in future studies of sarcoidosis. RECENT FINDINGS The clinical manifestations of sarcoidosis differ based on sex and gender There is emerging evidence that female and male hormones and X-linked genes are important determinants of immune responses to environmental antigens, which has important implications for granuloma formation in the context of sarcoidosis Furthermore, sex hormone levels predictably change throughout adolescence and adulthood, and this occurs in parallel with the onset immune senescence and changes in physiology with advanced age. SUMMARY Recent studies indicate that sex and age are important variables shaping the immune response of humans to environmental antigens We posit herein that sex and age are important determinants of sarcoidosis clinical phenotypes Many gaps in our understanding of the roles played by sex and gender in sarcoidosis, and these need to be considered in future studies.
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Affiliation(s)
- Arindam Singha
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, Ohio
| | - Marina Kirkland
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Wonder Drake
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Elliott D Crouser
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University, Columbus, Ohio
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17
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Wang C, Lashua LP, Carter CE, Johnson SK, Wang M, Ross TM, Ghedin E, Zhang B, Forst CV. Sex disparities in influenza: A multiscale network analysis. iScience 2022; 25:104192. [PMID: 35479404 PMCID: PMC9036134 DOI: 10.1016/j.isci.2022.104192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 12/05/2021] [Accepted: 03/30/2022] [Indexed: 12/12/2022] Open
Abstract
Sex differences in the pathogenesis of infectious diseases because of differential immune responses between females and males have been well-documented for multiple pathogens. However, the molecular mechanism underlying the observed sex differences in influenza virus infection remains poorly understood. In this study, we used a network-based approach to characterize the blood transcriptome collected over the course of infection with influenza A virus from female and male ferrets to dissect sex-biased gene expression. We identified significant differences in the temporal dynamics and regulation of immune responses between females and males. Our results elucidate sex-differentiated pathways involved in the unfolded protein response (UPR), lipid metabolism, and inflammatory responses, including a female-biased IRE1/XBP1 activation and male-biased crosstalk between metabolic reprogramming and IL-1 and AP-1 pathways. Overall, our study provides molecular insights into sex differences in transcriptional regulation of immune responses and contributes to a better understanding of sex biases in influenza pathogenesis. Regulation of immune responses between females and males is significantly different Rapid activation of UPR in females triggers potent immune and inflammatory responses Male-specific regulatory pattern in the AP1 pathway indicate a bias in immune response
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Affiliation(s)
- Chang Wang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Lauren P. Lashua
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Chalise E. Carter
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Scott K. Johnson
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029-6574, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029-6501, USA
| | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Systems Genomics Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029-6574, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029-6501, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, NY 10029-6574, USA
| | - Christian V. Forst
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029-6574, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029-6501, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY 10029-6574
- Corresponding author
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18
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Lorenz M, Witt E, Völker U, Stangl K, Stangl V, Hammer E. Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs. Proteomics 2022; 22:e2100168. [PMID: 35357760 DOI: 10.1002/pmic.202100168] [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: 07/21/2021] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022]
Abstract
There is growing evidence for sex and gender differences in the clinical manifestation and outcomes of human diseases. Human primary endothelial cells represent a useful cardiovascular model to study sexual dimorphisms at the cellular level. Here, we analyzed sexual dimorphisms of the secretome after serum starvation using HUVECs from twin pairs of the opposite sex to minimize the impact of varying genetic background. HUVECs were starved for 5 and 16 h, respectively, and proteins of the cell culture supernatants were analyzed by tandem mass spectrometry. Altogether, 960 extracellular proteins were identified of which 683 were amendable to stringent quantification. Significant alterations were observed for 324 proteins between long-term and short-term starvation and the majority were similar in both sexes. Only 5 proteins showed significant sex-specific regulation between long- versus short-term starvation. Furthermore, 19 unique proteins with significant sexual dimorphisms at the same time points of serum starvation were observed. A larger number of proteins, e.g. tissue factor inhibitor 2 (TFPI2), displayed higher levels in the supernatants of females compared to male cells after long term serum starvation that might point to higher adaptation capacity of female cells. The overall results demonstrate that male and female cells differ in their secretome. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mario Lorenz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medizinische Klinik für Kardiologie und Angiologie, Campus Mitte, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin
| | - Eric Witt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Greifswald
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Greifswald
| | - Karl Stangl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medizinische Klinik für Kardiologie und Angiologie, Campus Mitte, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin
| | - Verena Stangl
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Medizinische Klinik für Kardiologie und Angiologie, Campus Mitte, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin
| | - Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Greifswald
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19
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Long non-coding RNA Xist contribution in systemic lupus erythematosus and rheumatoid arthritis. Clin Immunol 2022; 236:108937. [PMID: 35114365 DOI: 10.1016/j.clim.2022.108937] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
Abstract
Growing evidence points towards the role of the long non-coding (lnc)-RNA Xist expressed in female cells as a predominant key actor for the sex bias observed in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Indeed, in female cells, lnc-Xist controls transcription directly by spreading across the inactivated X chromosome (Xi) and indirectly by sequestring miRNAs as a sponge. The inactivation process at Xi is altered in lymphocytes from SLE women and associated with important variations in ribonucleoproteins (RNP) associated with lnc-Xist. In fibroblast-like synoviocytes (FLS) and osteoclasts from RA women, proinflammatory and proliferative pathways are upregulated due to the sequestration effect exerted by lnc-Xist overexpression on miRNAs. The key role played by lnc-Xist in SLE and RA is further supported by it's knock down that recapitulates the SLE B cell extrafollicular profile and controls RA associated FLS proinflammatory cytokine production and proliferation.
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20
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Sex differences in the genetic regulation of the blood transcriptome response to glucocorticoid receptor activation. Transl Psychiatry 2021; 11:632. [PMID: 34903727 PMCID: PMC8669026 DOI: 10.1038/s41398-021-01756-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Substantial sex differences have been reported in the physiological response to stress at multiple levels, including the release of the stress hormone, cortisol. Here, we explore the genomic variants in 93 females and 196 males regulating the initial transcriptional response to cortisol via glucocorticoid receptor (GR) activation. Gene expression levels in peripheral blood were obtained before and after GR-stimulation with the selective GR agonist dexamethasone to identify differential expression following GR-activation. Sex stratified analyses revealed that while the transcripts responsive to GR-stimulation were mostly overlapping between males and females, the quantitative trait loci (eQTLs) regulation differential transcription to GR-stimulation was distinct. Sex-stratified eQTL SNPs (eSNPs) were located in different functional genomic elements and sex-stratified transcripts were enriched within postmortem brain transcriptional profiles associated with Major Depressive Disorder (MDD) specifically in males and females in the cingulate cortex. Female eSNPs were enriched among SNPs linked to MDD in genome-wide association studies. Finally, transcriptional sensitive genetic profile scores derived from sex-stratified eSNPS regulating differential transcription to GR-stimulation were predictive of depression status and depressive symptoms in a sex-concordant manner in a child and adolescent cohort (n = 584). These results suggest the potential of eQTLs regulating differential transcription to GR-stimulation as biomarkers of sex-specific biological risk for stress-related psychiatric disorders.
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21
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Zhao J, Zhou YH, Zhao YQ, Feng Y, Yan F, Gao ZR, Ye Q, Chen Y, Liu Q, Tan L, Zhang SH, Hu J, Dusenge MA, Feng YZ, Guo Y. Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis. J Immunol Res 2021; 2021:7403042. [PMID: 34859107 PMCID: PMC8632398 DOI: 10.1155/2021/7403042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/30/2021] [Indexed: 01/11/2023] Open
Abstract
Periodontitis is a globally prevalent disease that imposes a functional and aesthetic burden on patients. The oral microbiome influences human health. The aim of this study was at assessing gender variation in the subgingival bacterial microbiome of elderly patients with initial periodontitis and to determine the causes of this variation. Twelve males and twenty females (range 50-68 years old) with initial periodontitis provided subgingival plaque samples. 16S rRNA gene sequencing, QIIME-based data processing, and statistical analyses were carried out using several different analytical approaches to detect differences in the oral microbiome between the two groups. Males had higher Chao1 index, observed species, and phylogenetic diversity whole tree values than females. Analysis of β-diversity indicated that the samples were reasonably divided by the gender. The linear discriminant analysis effect size showed that the most representative biomarkers were the genus Haemophilus in males, whereas the dominant bacteria in females were Campylobacter. Kyoto Encyclopedia of Genes and Genomes analysis showed that predicting changes in the female oral microbiota may be related to the immune system and immune system diseases are the main factor in males. These data suggest that gender may be a differentiating factor in the microbial composition of subgingival plaques in elderly patients with initial periodontitis. These results could deepen our understanding of the role of gender in the oral microbiota present during initial periodontitis.
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Affiliation(s)
- Jie Zhao
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Ying-Hui Zhou
- National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Ya-Qiong Zhao
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Yao Feng
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Fei Yan
- Hunan Key Laboratory of Oral Health Research & Hunan 3D Printing Engineering Research Center of Oral Care & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha 410008, China
| | - Zheng-Rong Gao
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Qin Ye
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Yun Chen
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Qiong Liu
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Li Tan
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Shao-Hui Zhang
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Jing Hu
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Marie Aimee Dusenge
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Yun-Zhi Feng
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital of Central South University, Changsha, 410011 Hunan, China
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22
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Gevezova M, Sarafian V, Anderson G, Maes M. Inflammation and Mitochondrial Dysfunction in Autism Spectrum Disorder. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2021; 19:320-333. [PMID: 32600237 DOI: 10.2174/1871527319666200628015039] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/30/2020] [Accepted: 05/01/2020] [Indexed: 12/11/2022]
Abstract
Autism Spectrum Disorders (ASD) is a severe childhood psychiatric condition with an array of cognitive, language and social impairments that can significantly impact family life. ASD is classically characterized by reduced communication skills and social interactions, with limitations imposed by repetitive patterns of behavior, interests, and activities. The pathophysiology of ASD is thought to arise from complex interactions between environmental and genetic factors within the context of individual development. A growing body of research has raised the possibility of identifying the aetiological causes of the disorder. This review highlights the roles of immune-inflammatory pathways, nitro-oxidative stress and mitochondrial dysfunctions in ASD pathogenesis and symptom severity. The role of NK-cells, T helper, T regulatory and B-cells, coupled with increased inflammatory cytokines, lowered levels of immune-regulatory cytokines, and increased autoantibodies and microglial activation is elucidated. It is proposed that alterations in mitochondrial activity and nitrooxidative stress are intimately associated with activated immune-inflammatory pathways. Future research should determine as to whether the mitochondria, immune-inflammatory activity and nitrooxidative stress changes in ASD affect the development of amygdala-frontal cortex interactions. A number of treatment implications may arise, including prevention-orientated prenatal interventions, treatment of pregnant women with vitamin D, and sodium butyrate. Treatments of ASD children and adults with probiotics, sodium butyrate and butyrate-inducing diets, antipurinergic therapy with suramin, melatonin, oxytocin and taurine are also discussed.
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Affiliation(s)
- Maria Gevezova
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria,Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria,Research Institute at Medical University-Plovdiv, Plovdiv, Bulgaria
| | | | - Michael Maes
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria,Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand,IMPACT Strategic Research Center, Deakin University, Geelong, Australia
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23
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Bernabeu E, Canela-Xandri O, Rawlik K, Talenti A, Prendergast J, Tenesa A. Sex differences in genetic architecture in the UK Biobank. Nat Genet 2021; 53:1283-1289. [PMID: 34493869 DOI: 10.1038/s41588-021-00912-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/12/2021] [Indexed: 01/05/2023]
Abstract
Males and females present differences in complex traits and in the risk of a wide array of diseases. Genotype by sex (GxS) interactions are thought to account for some of these differences. However, the extent and basis of GxS are poorly understood. In the present study, we provide insights into both the scope and the mechanism of GxS across the genome of about 450,000 individuals of European ancestry and 530 complex traits in the UK Biobank. We found small yet widespread differences in genetic architecture across traits. We also found that, in some cases, sex-agnostic analyses may be missing trait-associated loci and looked into possible improvements in the prediction of high-level phenotypes. Finally, we studied the potential functional role of the differences observed through sex-biased gene expression and gene-level analyses. Our results suggest the need to consider sex-aware analyses for future studies to shed light onto possible sex-specific molecular mechanisms.
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Affiliation(s)
- Elena Bernabeu
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Oriol Canela-Xandri
- Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Andrea Talenti
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - James Prendergast
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, UK.
- Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
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24
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So J, Tai AK, Lichtenstein AH, Wu D, Lamon-Fava S. Sexual dimorphism of monocyte transcriptome in individuals with chronic low-grade inflammation. Biol Sex Differ 2021; 12:43. [PMID: 34321081 PMCID: PMC8320037 DOI: 10.1186/s13293-021-00387-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/15/2021] [Indexed: 01/29/2023] Open
Abstract
Sexual dimorphism in the immune system is evidenced by a higher prevalence of autoimmune diseases in women and higher susceptibility to infectious diseases in men. However, the molecular basis of these sex-based differences is not fully understood. We have characterized the transcriptome profiles of peripheral blood monocytes from males and postmenopausal females with chronic low-grade inflammation. We identified 41 sexually differentially expressed genes [adjusted p value (FDR) < 0.1], including genes involved in immune cell activation (e.g., CEACAM1, FCGR2B, and SLAMF7) and antigen presentation (e.g., AIM2, CD1E, and UBA1) with a higher expression in females than males. Moreover, signaling pathways of immune or inflammatory responses, including interferon (IFN) signaling [z-score = 2.45, -log(p) = 3.88], were found to be more upregulated in female versus male monocytes, based on a set of genes exhibiting sex-biased expression (p < 0.03). The contribution of IFN signaling to the sexual transcriptional differences was further confirmed by direct comparisons of the monocyte sex-biased genes with IFN signature genes (ISGs) that were previously curated in mouse macrophages. ISGs showed a greater overlap with female-biased genes than male-biased genes and a higher overall expression in female than male monocytes, particularly for the genes of antiviral and inflammatory responses to IFN. Given the role of IFN in immune defense and autoimmunity, our results suggest that sexual dimorphism in immune functions may be associated with more priming of innate immune pathways in female than male monocytes. These findings highlight the role of sex on the human immune transcriptome.
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Affiliation(s)
- Jisun So
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Albert K Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | - Alice H Lichtenstein
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Dayong Wu
- Nutritional Immunology Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Stefania Lamon-Fava
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA.
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25
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Cole JJ, McColl A, Shaw R, Lynall ME, Cowen PJ, de Boer P, Drevets WC, Harrison N, Pariante C, Pointon L, Goodyear C, Bullmore E, Cavanagh J. No evidence for differential gene expression in major depressive disorder PBMCs, but robust evidence of elevated biological ageing. Transl Psychiatry 2021; 11:404. [PMID: 34294682 PMCID: PMC8298604 DOI: 10.1038/s41398-021-01506-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/20/2021] [Accepted: 06/10/2021] [Indexed: 12/30/2022] Open
Abstract
The increasingly compelling data supporting the involvement of immunobiological mechanisms in Major Depressive Disorder (MDD) might provide some explanation forthe variance in this heterogeneous condition. Peripheral blood measures of cytokines and chemokines constitute the bulk of evidence, with consistent meta-analytic data implicating raised proinflammatory cytokines such as IL6, IL1β and TNF. Among the potential mechanisms linking immunobiological changes to affective neurobiology is the accelerated biological ageing seen in MDD, particularly via the senescence associated secretory phenotype (SASP). However, the cellular source of immunobiological markers remains unclear. Pre-clinical evidence suggests a role for peripheral blood mononuclear cells (PBMC), thus here we aimed to explore the transcriptomic profile using RNA sequencing in PBMCs in a clinical sample of people with various levels of depression and treatment response comparing it with that in healthy controls (HCs). There were three groups with major depressive disorder (MDD): treatment-resistant (n = 94), treatment-responsive (n = 47) and untreated (n = 46). Healthy controls numbered 44. Using PBMCs gene expression analysis was conducted using RNAseq to a depth of 54.5 million reads. Differential gene expression analysis was performed using DESeq2. The data showed no robust signal differentiating MDD and HCs. There was, however, significant evidence of elevated biological ageing in MDD vs HC. Biological ageing was evident in these data as a transcriptional signature of 888 age-associated genes (adjusted p < 0.05, absolute log2fold > 0.6) that also correlated strongly with chronological age (spearman correlation coefficient of 0.72). Future work should expand clinical sample sizes and reduce clinical heterogeneity. Exploration of RNA-seq signatures in other leukocyte populations and single cell RNA sequencing may help uncover more subtle differences. However, currently the subtlety of any PBMC signature mitigates against its convincing use as a diagnostic or predictive biomarker.
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Affiliation(s)
- John J. Cole
- grid.8756.c0000 0001 2193 314XInstitute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Alison McColl
- grid.8756.c0000 0001 2193 314XInstitute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Robin Shaw
- grid.23636.320000 0000 8821 5196Cancer Research UK Beatson Institute, Glasgow, UK
| | - Mary-Ellen Lynall
- grid.5335.00000000121885934Department of Psychiatry, University of Cambridge, UK and Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Philip J. Cowen
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, CB2 0SZ UK
| | - Peter de Boer
- grid.419619.20000 0004 0623 0341Janssen Research and Development, Experimental Medicine-Neuroscience Therapeutic Area, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Wayne C. Drevets
- grid.497530.c0000 0004 0389 4927Neuroscience Therapeutic Area, Janssen Research & Development, LLC, San Diego, CA USA
| | - Neil Harrison
- grid.5600.30000 0001 0807 5670Cardiff University Brain Research Imaging Centre, Maindy Road, Cardiff, UK
| | - Carmine Pariante
- grid.13097.3c0000 0001 2322 6764Stress, Psychiatry and Immunology Laboratory & Section of Perinatal Psychiatry, King’s College, University of London, London, UK
| | - Linda Pointon
- grid.5335.00000000121885934Department of Psychiatry, University of Cambridge, UK and Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | | | - Carl Goodyear
- grid.8756.c0000 0001 2193 314XInstitute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Edward Bullmore
- grid.5335.00000000121885934Department of Psychiatry, University of Cambridge, UK and Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Jonathan Cavanagh
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK.
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26
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Y disruption, autosomal hypomethylation and poor male lung cancer survival. Sci Rep 2021; 11:12453. [PMID: 34127738 PMCID: PMC8203787 DOI: 10.1038/s41598-021-91907-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/26/2021] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the most frequent cause of cancer death worldwide. It affects more men than women, and men generally have worse survival outcomes. We compared gene co-expression networks in affected and unaffected lung tissue from 126 consecutive patients with Stage IA-IV lung cancer undergoing surgery with curative intent. We observed marked degradation of a sex-associated transcription network in tumour tissue. This disturbance, detected in 27.7% of male tumours in the discovery dataset and 27.3% of male tumours in a further 123-sample replication dataset, was coincident with partial losses of the Y chromosome and extensive autosomal DNA hypomethylation. Central to this network was the epigenetic modifier and regulator of sexually dimorphic gene expression, KDM5D. After accounting for prognostic and epidemiological covariates including stage and histology, male patients with tumour KDM5D deficiency showed a significantly increased risk of death (Hazard Ratio [HR] 3.80, 95% CI 1.40-10.3, P = 0.009). KDM5D deficiency was confirmed as a negative prognostic indicator in a further 1100 male lung tumours (HR 1.67, 95% CI 1.4-2.0, P = 1.2 × 10-10). Our findings identify tumour deficiency of KDM5D as a prognostic marker and credible mechanism underlying sex disparity in lung cancer.
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27
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Wang J, Lan Y, He L, Tang R, Li Y, Huang Y, Liang S, Gao Z, Price M, Yue B, He M, Guo T, Fan Z. Sex-specific gene expression in the blood of four primates. Genomics 2021; 113:2605-2613. [PMID: 34116169 DOI: 10.1016/j.ygeno.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/03/2021] [Accepted: 06/06/2021] [Indexed: 10/21/2022]
Abstract
Blood is an important non-reproductive tissue, but little is known about the sex-specific gene expressions in the blood. Therefore, we investigated sex-specific gene expression differences in the blood tissues of four primates, rhesus macaques (Macaca mulatta), Tibetan macaques (M. thibetana), yellow baboons (Papio cynocephalus), and humans. We identified seven sex-specific differentially expressed genes (SDEGs) in each non-human primate and 31 SDEGs in humans. The four primates had only one common SDEG, MAP7D2. In humans, immune-related SDEGs were identified as up-regulated, but also down-regulated in females. We also found that most of the X-Y gene pairs had similar expression levels between species, except pair EIF1AY/EIF1AX. The expression level of X-Y gene pairs of rhesus and Tibetan macaques showed no significant differential expression levels, while humans had six significant XY-biased and three XX-biased X-Y gene pairs. Our observed sex differences in blood should increase understanding of sex differences in primate blood tissue.
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Affiliation(s)
- Jiao Wang
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yue Lan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Lewei He
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ruixiang Tang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Yuhui Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Yuan Huang
- Medical Laboratory Department of West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Shan Liang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Zhan Gao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China
| | - Megan Price
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu 610052, Sichuan, China.
| | - Tao Guo
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China.
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28
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Kuan PF, Yang X, Ren X, Che C, Waszczuk M, Kotov R, Clouston S, Singh PK, Glenn ST, Gomez EC, Wang J, Bromet E, Luft BJ. Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders. Transl Psychiatry 2021; 11:310. [PMID: 34031375 PMCID: PMC8144574 DOI: 10.1038/s41398-021-01431-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023] Open
Abstract
Gene expression has provided promising insights into the pathophysiology of post-traumatic stress disorder (PTSD); however, specific regulatory transcriptomic mechanisms remain unknown. The present study addressed this limitation by performing transcriptome-wide RNA-Seq of whole-blood samples from 226 World Trade Center responders. The investigation focused on differential expression (DE) at the gene, isoform, and for the first time, alternative splicing (AS) levels associated with the symptoms of PTSD: total burden, re-experiencing, avoidance, numbing, and hyperarousal subdimensions. These symptoms were associated with 76, 1, 48, 15, and 49 DE genes, respectively (FDR < 0.05). Moreover, they were associated with 103, 11, 0, 43, and 32 AS events. Avoidance differed the most from other dimensions with respect to DE genes and AS events. Gene set enrichment analysis (GSEA) identified pathways involved in inflammatory and metabolic processes, which may have implications in the treatment of PTSD. Overall, the findings shed a novel light on the wide range of transcriptomic alterations associated with PTSD at the gene and AS levels. The results of DE analysis associated with PTSD subdimensions highlights the importance of studying PTSD symptom heterogeneity.
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Affiliation(s)
- Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.
| | - Xiaohua Yang
- grid.36425.360000 0001 2216 9681Department of Medicine, Stony Brook University, Stony Brook, NY USA
| | - Xu Ren
- grid.36425.360000 0001 2216 9681Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY USA
| | - Chang Che
- grid.36425.360000 0001 2216 9681Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY USA
| | - Monika Waszczuk
- grid.262641.50000 0004 0388 7807Department of Psychology, Rosalind Franklin University of Medicine and Science, North Chicago, IL USA
| | - Roman Kotov
- Department of Psychiatry, Stony Book University, Stony Brook, NY USA
| | - Sean Clouston
- Department of Family and Preventive Medicine, Stony Book University, Stony Brook, NY USA
| | - Prashant K. Singh
- grid.240614.50000 0001 2181 8635Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Sean T. Glenn
- grid.240614.50000 0001 2181 8635Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Eduardo Cortes Gomez
- grid.240614.50000 0001 2181 8635Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Jianmin Wang
- grid.240614.50000 0001 2181 8635Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Evelyn Bromet
- Department of Psychiatry, Stony Book University, Stony Brook, NY USA
| | - Benjamin J. Luft
- grid.36425.360000 0001 2216 9681Department of Medicine, Stony Brook University, Stony Brook, NY USA
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29
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Li HJ, Su X, Zhang LW, Zhang CY, Wang L, Li WQ, Yang YF, Lv LX, Li M, Xiao X. Transcriptomic analyses of humans and mice provide insights into depression. Zool Res 2021; 41:632-643. [PMID: 32987454 PMCID: PMC7671914 DOI: 10.24272/j.issn.2095-8137.2020.174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Accumulating studies have been conducted to identify risk genes and relevant biological mechanisms underlying major depressive disorder (MDD). In particular, transcriptomic analyses in brain regions engaged in cognitive and emotional processes, e.g., the dorsolateral prefrontal cortex (DLPFC), have provided essential insights. Based on three independent DLPFC RNA-seq datasets of 79 MDD patients and 75 healthy controls, we performed differential expression analyses using two alternative approaches for cross-validation. We also conducted transcriptomic analyses in mice undergoing chronic variable stress (CVS) and chronic social defeat stress (CSDS). We identified 12 differentially expressed genes (DEGs) through both analytical methods in MDD patients, the majority of which were also dysregulated in stressed mice. Notably, the mRNA level of the immediate early gene FOS ( Fos proto-oncogene) was significantly decreased in both MDD patients and CVS-exposed mice, and CSDS-susceptible mice exhibited a greater reduction in Fos expression compared to resilient mice. These findings suggest the potential key roles of this gene in the pathogenesis of MDD related to stress exposure. Altered transcriptomes in the DLPFC of MDD patients might be, at least partially, the result of stress exposure, supporting that stress is a primary risk factor for MDD.
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Affiliation(s)
- Hui-Juan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Xi Su
- Henan Mental Hospital, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453002, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan 453002, China
| | - Lu-Wen Zhang
- Henan Mental Hospital, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453002, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan 453002, China
| | - Chu-Yi Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Lu Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wen-Qiang Li
- Henan Mental Hospital, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453002, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan 453002, China
| | - Yong-Feng Yang
- Henan Mental Hospital, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453002, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan 453002, China
| | - Lu-Xian Lv
- Henan Mental Hospital, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan 453002, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan 453002, China.,Henan Province People's Hospital, Zhengzhou, Henan 450003, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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Kuan P, Clouston S, Yang X, Che C, Gandy S, Kotov R, Bromet E, Luft BJ. Single-cell transcriptomics analysis of mild cognitive impairment in World Trade Center disaster responders. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12154. [PMID: 33665344 PMCID: PMC7896635 DOI: 10.1002/dad2.12154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Recent research has found that World Trade Center (WTC) responders in their mid-50s have an elevated prevalence of mild cognitive impairment (MCI) that is associated with neural degeneration and subcortical thinning. This article extends our understanding of the molecular complexity of MCI through gene expression profiling of blood. METHODS The transcriptomics of 40 male WTC responders were profiled across two cohorts (discovery: nine MCI and nine controls; replication: 11 MCI and 11 controls) using CITE-Seq at single-cell resolution in blood. RESULTS Comparing the transcriptomic signatures across seven major cell subpopulations, the largest differences were observed in monocytes in which 226 genes were differentially expressed. Pathway analysis on the genes unique to monocytes identified processes associated with cerebral immune response. DISCUSSION Our findings suggested monocytes may constitute a key cell type to target in blood-based biomarker studies for early detection of risk of MCI and development of new interventions.
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Affiliation(s)
- Pei‐Fen Kuan
- Department of Applied Mathematics and StatisticsStony Brook UniversityStony BrookNew YorkUSA
| | - Sean Clouston
- Department of Family and Preventive MedicineStony Book UniversityStony BrookNew YorkUSA
| | - Xiaohua Yang
- Department of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Chang Che
- Department of Applied Mathematics and StatisticsStony Brook UniversityStony BrookNew YorkUSA
| | - Samuel Gandy
- Department of NeurologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Roman Kotov
- Department of PsychiatryStony Book UniversityStony BrookNew YorkUSA
| | - Evelyn Bromet
- Department of PsychiatryStony Book UniversityStony BrookNew YorkUSA
| | - Benjamin J. Luft
- Department of MedicineStony Brook UniversityStony BrookNew YorkUSA
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31
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Jansen R, Han LK, Verhoeven JE, Aberg KA, van den Oord EC, Milaneschi Y, Penninx BW. An integrative study of five biological clocks in somatic and mental health. eLife 2021; 10:59479. [PMID: 33558008 PMCID: PMC7872513 DOI: 10.7554/elife.59479] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
Biological clocks have been developed at different molecular levels and were found to be more advanced in the presence of somatic illness and mental disorders. However, it is unclear whether different biological clocks reflect similar aging processes and determinants. In ~3000 subjects, we examined whether five biological clocks (telomere length, epigenetic, transcriptomic, proteomic, and metabolomic clocks) were interrelated and associated to somatic and mental health determinants. Correlations between biological aging indicators were small (all r < 0.2), indicating little overlap. The most consistent associations of advanced biological aging were found for male sex, higher body mass index (BMI), metabolic syndrome, smoking, and depression. As compared to the individual clocks, a composite index of all five clocks showed most pronounced associations with health determinants. The large effect sizes of the composite index and the low correlation between biological aging indicators suggest that one's biological age is best reflected by combining aging measures from multiple cellular levels.
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Affiliation(s)
- Rick Jansen
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Laura Km Han
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Josine E Verhoeven
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, United States
| | - Edwin Cgj van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, United States
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Brenda Wjh Penninx
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, Netherlands
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32
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Seifert S, Gundlach S, Junge O, Szymczak S. Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. Bioinformatics 2021; 36:4301-4308. [PMID: 32399562 PMCID: PMC7520048 DOI: 10.1093/bioinformatics/btaa483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION High-throughput technologies allow comprehensive characterization of individuals on many molecular levels. However, training computational models to predict disease status based on omics data is challenging. A promising solution is the integration of external knowledge about structural and functional relationships into the modeling process. We compared four published random forest-based approaches using two simulation studies and nine experimental datasets. RESULTS The self-sufficient prediction error approach should be applied when large numbers of relevant pathways are expected. The competing methods hunting and learner of functional enrichment should be used when low numbers of relevant pathways are expected or the most strongly associated pathways are of interest. The hybrid approach synthetic features is not recommended because of its high false discovery rate. AVAILABILITY AND IMPLEMENTATION An R package providing functions for data analysis and simulation is available at GitHub (https://github.com/szymczak-lab/PathwayGuidedRF). An accompanying R data package (https://github.com/szymczak-lab/DataPathwayGuidedRF) stores the processed and quality controlled experimental datasets downloaded from Gene Expression Omnibus (GEO). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stephan Seifert
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Sven Gundlach
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
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33
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Shepherd R, Cheung AS, Pang K, Saffery R, Novakovic B. Sexual Dimorphism in Innate Immunity: The Role of Sex Hormones and Epigenetics. Front Immunol 2021; 11:604000. [PMID: 33584674 PMCID: PMC7873844 DOI: 10.3389/fimmu.2020.604000] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Sexual dimorphism refers to differences between biological sexes that extend beyond sexual characteristics. In humans, sexual dimorphism in the immune response has been well demonstrated, with females exhibiting lower infection rates than males for a variety of bacterial, viral, and parasitic pathogens. There is also a substantially increased incidence of autoimmune disease in females compared to males. Together, these trends indicate that females have a heightened immune reactogenicity to both self and non-self-molecular patterns. However, the molecular mechanisms driving the sexually dimorphic immune response are not fully understood. The female sex hormones estrogen and progesterone, as well as the male androgens, such as testosterone, elicit direct effects on the function and inflammatory capacity of immune cells. Several studies have identified a sex-specific transcriptome and methylome, independent of the well-described phenomenon of X-chromosome inactivation, suggesting that sexual dimorphism also occurs at the epigenetic level. Moreover, distinct alterations to the transcriptome and epigenetic landscape occur in synchrony with periods of hormonal change, such as puberty, pregnancy, menopause, and exogenous hormone therapy. These changes are also mirrored by changes in immune cell function. This review will outline the evidence for sex hormones and pregnancy-associated hormones as drivers of epigenetic change, and how this may contribute to the sexual dimorphism. Determining the effects of sex hormones on innate immune function is important for understanding sexually dimorphic autoimmune diseases, sex-specific responses to pathogens and vaccines, and how innate immunity is altered during periods of hormonal change (endogenous or exogenous).
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Affiliation(s)
- Rebecca Shepherd
- Epigenetics Group, Infection and Immunity Theme, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Ada S. Cheung
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia
- Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Ken Pang
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Brain and Mitochondrial Research, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Adolescent Medicine, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Richard Saffery
- Epigenetics Group, Infection and Immunity Theme, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Boris Novakovic
- Epigenetics Group, Infection and Immunity Theme, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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34
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Sex-specific differences in peripheral blood leukocyte transcriptional response to LPS are enriched for HLA region and X chromosome genes. Sci Rep 2021; 11:1107. [PMID: 33441806 PMCID: PMC7806814 DOI: 10.1038/s41598-020-80145-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
Sex-specific differences in prevalence are well documented for many common, complex diseases, especially for immune-mediated diseases, yet the precise mechanisms through which factors associated with biological sex exert their effects throughout life are not well understood. We interrogated sex-specific transcriptional responses of peripheral blood leukocytes (PBLs) to innate immune stimulation by lipopolysaccharide (LPS) in 46 male and 66 female members of the Hutterite community, who practice a communal lifestyle. We identified 1217 autosomal and 54 X-linked genes with sex-specific responses to LPS, as well as 71 autosomal and one X-linked sex-specific expression quantitative trait loci (eQTLs). Despite a similar proportion of the 15 HLA genes responding to LPS compared to all expressed autosomal genes, there was a significant over-representation of genes with sex by treatment interactions among HLA genes. We also observed an enrichment of sex-specific differentially expressed genes in response to LPS for X-linked genes compared to autosomal genes, suggesting that HLA and X-linked genes may disproportionately contribute to sex disparities in risk for immune-mediated diseases.
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35
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The Effects of Age, Cigarette Smoking, Sex, and Race on the Qualitative Characteristics of Lung Transcriptome. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6418460. [PMID: 32802863 PMCID: PMC7424369 DOI: 10.1155/2020/6418460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022]
Abstract
The within-sample relative expression orderings (REOs) of genes, which are stable qualitative transcriptional characteristics, can provide abundant information for a disease. Methods based on REO comparisons have been proposed for identifying differentially expressed genes (DEGs) at the individual level and for detecting disease-associated genes based on one-phenotype disease data by reusing data of normal samples from other sources. Here, we evaluated the effects of common potential confounding factors, including age, cigarette smoking, sex, and race, on the REOs of gene pairs within normal lung tissues transcriptome. Our results showed that age has little effect on REOs within lung tissues. We found that about 0.23% of the significantly stable REOs of gene pairs in nonsmokers' lung tissues are reversed in smokers' lung tissues, introduced by 344 DEGs between the two groups of samples (RankCompV2, FDR <0.05), which are enriched in metabolism of xenobiotics by cytochrome P450, glutathione metabolism, and other pathways (hypergeometric test, FDR <0.05). Comparison between the normal lung tissue samples of males and females revealed fewer reversal REOs introduced by 24 DEGs between the sex groups, among which 19 DEGs are located on sex chromosomes and 5 DEGs involving in spermatogenesis and regulation of oocyte are located on autosomes. Between the normal lung tissue samples of white and black people, we identified 22 DEGs (RankCompV2, FDR <0.05) which introduced a few reversal REOs between the two races. In summary, the REO-based study should take into account the confounding factors of cigarette smoking, sex, and race.
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36
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Credendino SC, Neumayer C, Cantone I. Genetics and Epigenetics of Sex Bias: Insights from Human Cancer and Autoimmunity. Trends Genet 2020; 36:650-663. [PMID: 32736810 DOI: 10.1016/j.tig.2020.06.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
High-throughput sequencing and genome-wide association studies have revealed a sex bias in human diseases. The underlying molecular mechanisms remain, however, unknown. Here, we cover recent advances in cancer and autoimmunity focusing on intrinsic genetic and epigenetic differences underlying sex biases in human disease. These studies reveal a central role of genome regulatory mechanisms including genome repair, chromosome folding, and epigenetic regulation in dictating the sex bias. These highlight the importance of considering sex as a variable in both basic science and clinical investigations. Understanding the molecular mechanisms underlying sex bias in human diseases will be instrumental in making a first step forwards into the era of personalized medicine.
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Affiliation(s)
- Sara Carmela Credendino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Christoph Neumayer
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Irene Cantone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; Institute of Experimental Endocrinology and Oncology 'G. Salvatore', National Research Council (CNR), 80131 Naples, Italy.
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37
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Hartman RJG, Kapteijn DMC, Haitjema S, Bekker MN, Mokry M, Pasterkamp G, Civelek M, den Ruijter HM. Intrinsic transcriptomic sex differences in human endothelial cells at birth and in adults are associated with coronary artery disease targets. Sci Rep 2020; 10:12367. [PMID: 32704153 PMCID: PMC7378217 DOI: 10.1038/s41598-020-69451-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023] Open
Abstract
Sex differences in endothelial cell (EC) biology may reflect intrinsic differences driven by chromosomes or sex steroid exposure and gender differences accumulated over life. We analysed EC gene expression data from boy-girl twins at birth and in non-twin adults to detect sex differences at different stages of life, and show that 14-25% of the EC transcriptome is sex-biased. By combining data from both stages of life, we identified sex differences that are present at birth and maintained throughout life, and those that are acquired over life. Promisingly, we found that genes that present with an acquired sex difference in ECs are more likely to be targets of sex steroids. Annotating both gene sets with data from multiple genome-wide association studies (GWAS) revealed that genes with an intrinsic sex difference in ECs are enriched for coronary artery disease GWAS hits. This study underscores the need for treating sex as a biological variable.
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Affiliation(s)
- Robin J G Hartman
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daniek M C Kapteijn
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Saskia Haitjema
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mireille N Bekker
- Department of Obstetrics and Gynecology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Michal Mokry
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mete Civelek
- Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands.
- Division of Heart and Lungs, Department of Experimental Cardiology, University Medical Center Utrecht, Heidelberglaan 100, PO Box 85500, 3508GA, Utrecht, The Netherlands.
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Zhuang QKW, Galvez JH, Xiao Q, AlOgayil N, Hyacinthe J, Taketo T, Bourque G, Naumova AK. Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver. Cells 2020; 9:E1436. [PMID: 32527045 PMCID: PMC7349295 DOI: 10.3390/cells9061436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Sex biases in the genome-wide distribution of DNA methylation and gene expression levels are some of the manifestations of sexual dimorphism in mammals. To advance our understanding of the mechanisms that contribute to sex biases in DNA methylation and gene expression, we conducted whole genome bisulfite sequencing (WGBS) as well as RNA-seq on liver samples from mice with different combinations of sex phenotype and sex-chromosome complement. We compared groups of animals with different sex phenotypes, but the same genetic sexes, and vice versa, same sex phenotypes, but different sex-chromosome complements. We also compared sex-biased DNA methylation in mouse and human livers. Our data show that sex phenotype, X-chromosome dosage, and the presence of Y chromosome shape the differences in DNA methylation between males and females. We also demonstrate that sex bias in autosomal methylation is associated with sex bias in gene expression, whereas X-chromosome dosage-dependent methylation differences are not, as expected for a dosage-compensation mechanism. Furthermore, we find partial conservation between the repertoires of mouse and human genes that are associated with sex-biased methylation, an indication that gene function is likely to be an important factor in this phenomenon.
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Affiliation(s)
- Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Qian Xiao
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA;
| | - Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
| | - Jeffrey Hyacinthe
- Department of Quantitative Life Sciences, McGill University, Montréal, QC H3A 0G4, Canada;
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada;
- Department of Surgery, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Anna K. Naumova
- Department of Human Genetics, McGill University, Montréal, QC H3A 1C7, Canada; (Q.K.-W.Z.); (N.A.)
- The Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada;
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC H4A 3J1, Canada
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Moore SR, Humphreys KL, Colich NL, Davis EG, Lin DTS, MacIsaac JL, Kobor MS, Gotlib IH. Distinctions between sex and time in patterns of DNA methylation across puberty. BMC Genomics 2020; 21:389. [PMID: 32493224 PMCID: PMC7268482 DOI: 10.1186/s12864-020-06789-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are significant sex differences in human physiology and disease; the genomic sources of these differences, however, are not well understood. During puberty, a drastic neuroendocrine shift signals physical changes resulting in robust sex differences in human physiology. Here, we explore how shifting patterns of DNA methylation may inform these pathways of biological plasticity during the pubertal transition. In this study we analyzed DNA methylation (DNAm) in saliva at two time points across the pubertal transition within the same individuals. Our purpose was to compare two domains of DNAm patterns that may inform processes of sexual differentiation 1) sex related sites, which demonstrated differences between males from females and 2) time related sites in which DNAm shifted significantly between timepoints. We further explored the correlated network structure sex and time related DNAm networks and linked these patterns to pubertal stage, assays of salivary testosterone, a reliable diagnostic of free, unbound hormone that is available to act on target tissues, and overlap with androgen response elements. RESULTS Sites that differed by biological sex were largely independent of sites that underwent change across puberty. Time-related DNAm sites, but not sex-related sites, formed correlated networks that were associated with pubertal stage. Both time and sex DNAm networks reflected salivary testosterone levels that were enriched for androgen response elements, with sex-related DNAm networks being informative of testosterone levels above and beyond biological sex later in the pubertal transition. CONCLUSIONS These results inform our understanding of the distinction between sex- and time-related differences in DNAm during the critical period of puberty and highlight a novel linkage between correlated patterns of sex-related DNAm and levels of salivary testosterone.
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Affiliation(s)
- Sarah Rose Moore
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.
| | - Kathryn Leigh Humphreys
- Department of Psychology and Human Development, Vanderbilt University, 230 Appleton Pl, Nashville, TN, 37203, USA
| | - Natalie Lisanne Colich
- Department of Psychology, University of Washington Seattle, Guthrie Hall (GTH), 119A 98195-1525, Seattle, WA, 98105, USA
| | - Elena Goetz Davis
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford, CA, 94305, USA
| | - David Tse Shen Lin
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Julia Lynn MacIsaac
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Michael Steffen Kobor
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Ian Henry Gotlib
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford, CA, 94305, USA
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Oertelt-Prigione S, Mariman E. The impact of sex differences on genomic research. Int J Biochem Cell Biol 2020; 124:105774. [PMID: 32470538 DOI: 10.1016/j.biocel.2020.105774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 01/23/2023]
Abstract
Sex and gender differences affect all dimensions of human health ranging from the biological basis of disease to therapeutic access, choice and response. Genomics research has long ignored the role of sex differences as potential modulators and the concept is gaining more attention only recently. In the present review we summarize the current knowledge of the impact of sex differences on genomic and epigenomic research, the potential interaction of genomics and gender and the role of these differences in disease etiopathogenesis. Sex differences can emerge from differences in the sex chromosomes themselves, from their interaction with the genome and from the influence of hormones on genomic processes. The impact of these processes on the incidence of autoimmune and oncologic disease is well documented. The growing field of systems biology, which aims at integrating information from different networks of the human body, could also greatly benefit from this approach. In the present review we summarize the current knowledge and provide recommendations for the future performance of sex-sensitive genomics research.
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Affiliation(s)
- Sabine Oertelt-Prigione
- Department of Primary and Community Care, Radboud Institute of Health Sciences, Radboudumc, Nijmegen, The Netherlands; Institute of Legal and Forensic Medicine, Charité - Universitätsmedizin, Berlin, Germany.
| | - Edwin Mariman
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
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Cloots K, Burza S, Malaviya P, Hasker E, Kansal S, Mollett G, Chakravarty J, Roy N, Lal BK, Rijal S, Sundar S, Boelaert M. Male predominance in reported Visceral Leishmaniasis cases: Nature or nurture? A comparison of population-based with health facility-reported data. PLoS Negl Trop Dis 2020; 14:e0007995. [PMID: 31995564 PMCID: PMC7010295 DOI: 10.1371/journal.pntd.0007995] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 02/10/2020] [Accepted: 12/09/2019] [Indexed: 12/20/2022] Open
Abstract
Background Bangladesh, India, and Nepal aim for the elimination of Visceral Leishmaniasis (VL), a systemic parasitic infectious disease, as a public health problem by 2020. For decades, male patients have comprised the majority of reported VL cases in this region. By comparing this reported VL sex ratio to the one observed in population-based studies conducted in the Indian subcontinent, we tested the working hypothesis that mainly socio-cultural gender differences in healthcare-seeking behavior explain this gender imbalance. Methodology/Principal findings We compared the observed sex ratio of male versus female among all VL cases reported by the health system in Nepal and in the two most endemic states in India with that observed in population-based cohort studies in India and Nepal. Also, we assessed male sex as a potential risk factor for seroprevalence at baseline, seroconversion, and VL incidence in the same population-based data. The male/female ratio among VL cases reported by the health systems was 1.40 (95% CI 1.37–1.43). In the population cohort data, the age- and study site-adjusted male to female risk ratio was 1.27 (95% CI 1.08–1.51). Also, males had a 19% higher chance of being seropositive at baseline in the population surveys (RR 1.19; 95% CI 1.11–1.27), while we observed no significant difference in seroconversion rate between both sexes at the DAT cut-off titer defined as the primary endpoint. Conclusions/Significance Our population-based data show that male sex is a risk factor for VL, and not only as a socio-cultural determinant. Biological sex-related differences likely play an important role in the pathogenesis of this disease. Visceral Leishmaniasis (VL) is a parasitic disease that is lethal if not treated timely and mainly affects impoverished populations. Bangladesh, India, and Nepal have targeted the elimination of this disease as a public health problem by 2020. The majority of VL patients attending the health services are male, and this is usually attributed to unequal access to health care for men and women in this sociocultural context. We analyzed two large datasets obtained in population surveillance projects, including regular door-to-door screening for VL, in India and Nepal. Thereby we minimized any potential differences in access to health care between both sexes, as every suspect VL case occurring in the community received a full diagnostic work-up, and the research project facilitated transport to treatment centers if needed. By comparing the observed sex ratio in the health services records with those of the population surveillance records, we aimed to reach meaningful conclusions about the pathway through which male gender exerts its leverage for increasing VL risk: socio-cultural determinants blocking women from accessing care (nurture) or biological factors (nature) making men more vulnerable to VL. Because in the population-based age adjusted-data, male VL cases were significantly more frequent than female, our findings strongly suggest that in the Indian subcontinent, biological differences between men and women play a more critical role in the pathogenesis of VL than previously assumed, and the observed male predominance in VL cases in health services cannot be explained by socio-cultural factors only. Moreover, data show that above the age of 14 years, males are seropositive more often than females and are at higher risk to develop VL disease.
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Affiliation(s)
- Kristien Cloots
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
| | | | | | - Epco Hasker
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sangeeta Kansal
- Department of Medicine, Banaras Hindu University, Varanasi, India
| | - Guy Mollett
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jaya Chakravarty
- Department of Medicine, Banaras Hindu University, Varanasi, India
| | - Nurpur Roy
- National Vector Borne Disease Control Program, Ministry of Health & Family Welfare, New Delhi, India
| | - Bibek Kumar Lal
- Epidemiology and Disease Control Division, Ministry of Health, Kathmandu, Nepal
| | - Suman Rijal
- Drugs for Neglected Diseases initiative, New Delhi, India
| | - Shyam Sundar
- Department of Medicine, Banaras Hindu University, Varanasi, India
| | - Marleen Boelaert
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
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42
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Scully EP, Gandhi M, Johnston R, Hoh R, Lockhart A, Dobrowolski C, Pagliuzza A, Milush JM, Baker CA, Girling V, Ellefson A, Gorelick R, Lifson J, Altfeld M, Alter G, Cedars M, Solomon A, Lewin SR, Karn J, Chomont N, Bacchetti P, Deeks SG. Sex-Based Differences in Human Immunodeficiency Virus Type 1 Reservoir Activity and Residual Immune Activation. J Infect Dis 2020; 219:1084-1094. [PMID: 30371873 DOI: 10.1093/infdis/jiy617] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/26/2018] [Indexed: 01/31/2023] Open
Abstract
Plasma human immunodeficiency virus type 1 (HIV-1) RNA levels in women are lower early in untreated HIV-1 infection compared with those in men, but women have higher T-cell activation and faster disease progression when adjusted for viral load. It is not known whether these sex differences persist during effective antiretroviral therapy (ART), or whether they would be relevant for the evaluation and implementation of HIV-1 cure strategies. We prospectively enrolled a cohort of reproductive-aged women and matched men on suppressive ART and measured markers of HIV-1 persistence, residual virus activity, and immune activation. The frequency of CD4+ T cells harboring HIV-1 DNA was comparable between the sexes, but there was higher cell-associated HIV-1 RNA, higher plasma HIV-1 (single copy assay), and higher T-cell activation and PD-1 expression in men compared with women. These sex-related differences in immune phenotype and HIV-1 persistence on ART have significant implications for the design and measurement of curative interventions.
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Affiliation(s)
- Eileen P Scully
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts.,Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Monica Gandhi
- Department of Medicine, University of California, San Francisco
| | | | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco
| | - Ainsley Lockhart
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge
| | | | - Amélie Pagliuzza
- Research Centre, Centre Hospitalier de l'Université de Montréal and Université de Montréal, Quebec, Canada
| | | | | | - Valerie Girling
- Department of Medicine, University of California, San Francisco
| | - Arlvin Ellefson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Maryland
| | - Jeffrey Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Maryland
| | | | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge
| | - Marcelle Cedars
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco
| | - Ajantha Solomon
- Peter Doherty Institute of Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Sharon R Lewin
- Peter Doherty Institute of Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | | | - Nicolas Chomont
- Research Centre, Centre Hospitalier de l'Université de Montréal and Université de Montréal, Quebec, Canada
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco
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43
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Rawat C, Kushwaha S, Srivastava AK, Kukreti R. Peripheral blood gene expression signatures associated with epilepsy and its etiologic classification. Genomics 2020; 112:218-224. [DOI: 10.1016/j.ygeno.2019.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/23/2019] [Accepted: 01/26/2019] [Indexed: 01/19/2023]
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44
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Bongen E, Lucian H, Khatri A, Fragiadakis GK, Bjornson ZB, Nolan GP, Utz PJ, Khatri P. Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection. Cell Rep 2019; 29:1961-1973.e4. [PMID: 31722210 PMCID: PMC6856718 DOI: 10.1016/j.celrep.2019.10.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 02/09/2023] Open
Abstract
Sex differences in autoimmunity and infection suggest that a better understanding of molecular sex differences will improve the diagnosis and treatment of immune-related disease. We identified 144 differentially expressed genes, referred to as immune sex expression signature (iSEXS), between human males and females using an integrated multi-cohort analysis of blood transcriptome profiles from six discovery cohorts from five continents with 458 healthy individuals. We validated iSEXS in 11 additional cohorts of 524 peripheral blood samples. When we separated iSEXS into genes located on sex chromosomes (XY-iSEXS) or autosomes (autosomal-iSEXS), both modules distinguished males and females. iSEXS reflects sex differences in immune cell proportions, with female-associated genes showing higher expression by CD4+ T cells and male-associated genes showing higher expression by myeloid cells. Autosomal-iSEXS detected an increase in monocytes with age in females, reflected sex-differential immune cell dynamics during influenza infection, and predicted antibody response in males, but not females.
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Affiliation(s)
- Erika Bongen
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Haley Lucian
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Avani Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zachary B Bjornson
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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45
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The Netherlands Twin Register: Longitudinal Research Based on Twin and Twin-Family Designs. Twin Res Hum Genet 2019; 22:623-636. [PMID: 31666148 DOI: 10.1017/thg.2019.93] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Netherlands Twin Register (NTR) is a national register in which twins, multiples and their parents, siblings, spouses and other family members participate. Here we describe the NTR resources that were created from more than 30 years of data collections; the development and maintenance of the newly developed database systems, and the possibilities these resources create for future research. Since the early 1980s, the NTR has enrolled around 120,000 twins and a roughly equal number of their relatives. The majority of twin families have participated in survey studies, and subsamples took part in biomaterial collection (e.g., DNA) and dedicated projects, for example, for neuropsychological, biomarker and behavioral traits. The recruitment into the NTR is all inclusive without any restrictions on enrollment. These resources - the longitudinal phenotyping, the extended pedigree structures and the multigeneration genotyping - allow for future twin-family research that will contribute to gene discovery, causality modeling, and studies of genetic and cultural inheritance.
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46
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Ouwens KG, Jansen R, Nivard MG, van Dongen J, Frieser MJ, Hottenga JJ, Arindrarto W, Claringbould A, van Iterson M, Mei H, Franke L, Heijmans BT, A C 't Hoen P, van Meurs J, Brooks AI, Penninx BWJH, Boomsma DI. A characterization of cis- and trans-heritability of RNA-Seq-based gene expression. Eur J Hum Genet 2019; 28:253-263. [PMID: 31558840 DOI: 10.1038/s41431-019-0511-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/21/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023] Open
Abstract
Insights into individual differences in gene expression and its heritability (h2) can help in understanding pathways from DNA to phenotype. We estimated the heritability of gene expression of 52,844 genes measured in whole blood in the largest twin RNA-Seq sample to date (1497 individuals including 459 monozygotic twin pairs and 150 dizygotic twin pairs) from classical twin modeling and identity-by-state-based approaches. We estimated for each gene h2total, composed of cis-heritability (h2cis, the variance explained by single nucleotide polymorphisms in the cis-window of the gene), and trans-heritability (h2res, the residual variance explained by all other genome-wide variants). Mean h2total was 0.26, which was significantly higher than heritability estimates earlier found in a microarray-based study using largely overlapping (>60%) RNA samples (mean h2 = 0.14, p = 6.15 × 10-258). Mean h2cis was 0.06 and strongly correlated with beta of the top cis expression quantitative loci (eQTL, ρ = 0.76, p < 10-308) and with estimates from earlier RNA-Seq-based studies. Mean h2res was 0.20 and correlated with the beta of the corresponding trans-eQTL (ρ = 0.04, p < 1.89 × 10-3) and was significantly higher for genes involved in cytokine-cytokine interactions (p = 4.22 × 10-15), many other immune system pathways, and genes identified in genome-wide association studies for various traits including behavioral disorders and cancer. This study provides a thorough characterization of cis- and trans-h2 estimates of gene expression, which is of value for interpretation of GWAS and gene expression studies.
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Affiliation(s)
- Klaasjan G Ouwens
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Rick Jansen
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maia J Frieser
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, USA.,Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wibowo Arindrarto
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, the Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, ErasmusMC, Rotterdam, The Netherlands
| | - Andrew I Brooks
- Department of Genetics and the Human Genetics Institute, RUCDR Infinite Biologics, Rutgers University, New Brunswick, NJ, USA
| | | | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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47
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ImmGen report: sexual dimorphism in the immune system transcriptome. Nat Commun 2019; 10:4295. [PMID: 31541153 PMCID: PMC6754408 DOI: 10.1038/s41467-019-12348-6] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/29/2019] [Indexed: 11/24/2022] Open
Abstract
Sexual dimorphism in the mammalian immune system is manifested as more frequent and severe infectious diseases in males and, on the other hand, higher rates of autoimmune disease in females, yet insights underlying those differences are still lacking. Here we characterize sex differences in the immune system by RNA and ATAC sequence profiling of untreated and interferon-induced immune cell types in male and female mice. We detect very few differentially expressed genes between male and female immune cells except in macrophages from three different tissues. Accordingly, very few genomic regions display differences in accessibility between sexes. Transcriptional sexual dimorphism in macrophages is mediated by genes of innate immune pathways, and increases after interferon stimulation. Thus, the stronger immune response of females may be due to more activated innate immune pathways prior to pathogen invasion. Sexual dimorphism is observed frequently in immune disorders, but the underlying insights are still unclear. Here the authors analyze transcriptome and epigenome changes induced by interferon in various mouse immune cell types, and find only a restricted set of sexual dimorphism genes in innate immunity and macrophages.
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48
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Peng X, Zhang Z, Ye D, Xing P, Zou Z, Lei H, Duan L. Gene dysregulation in peripheral blood of moyamoya disease and comparison with other vascular disorders. PLoS One 2019; 14:e0221811. [PMID: 31532776 PMCID: PMC6750579 DOI: 10.1371/journal.pone.0221811] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022] Open
Abstract
Objective Moyamoya disease (MMD) is a chronic occlusive cerebrovascular disease with unknown etiology, sharing many similar clinical symptoms with other vascular disorders. This study aimed to investigate gene dysregulation in peripheral blood of MMD and compare it with other vascular disorders. Methods Transcriptomic profiles of 12 MMD patients and 8 healthy controls were obtained using RNA sequencing. Differentially expressed genes (DEGs) were identified and several were validated by quantitative real-time PCR in independent samples. Biological pathway enrichment analysis of DEGs and deconvolution of leukocyte subsets in peripheral blood were performed. Expression profiles for other vascular diseases were downloaded from public database and consistent DEGs were calculated. Gene set enrichment analysis (GSEA) was conducted to compare gene dysregulation pattern between MMD and other vascular diseases. Results A total of 533 DEGs were identified for MMD. Up-regulated genes were mainly involved in extracellular matrix (ECM) organization, whereas down-regulated genes were primarily associated with inflammatory and immune responses. As for cell populations, significantly increased naïve B cells and naïve CD4 cells as well as obviously decreased resting natural killer cells were observed in peripheral blood of MMD patients. GSEA analysis indicated that only up-regulated genes of ischemic stroke and down-regulated genes of coronary artery disease and myocardial infarction were enriched in up-regulated and down-regulated genes of MMD, respectively. Conclusion Dysregulated genes in peripheral blood of MMD mainly played key roles in ECM organization, inflammatory and immune responses. This gene dysregulation pattern was specific compared with other vascular diseases. Besides, naïve B cells, naïve CD4 cells and resting natural killer cells were aberrantly disrupted in peripheral blood of MMD patients. These results will help elucidate the complicated pathogenic mechanism of MMD.
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Affiliation(s)
- Xing Peng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengshan Zhang
- Department of Neurosurgery, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Dongqing Ye
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Peiqi Xing
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengxing Zou
- Department of Neurosurgery, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Lian Duan
- Department of Neurosurgery, the Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
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49
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Voinsky I, McCarthy MJ, Shekhtman T, Kelsoe JR, Gurwitz D. SCN11A mRNA levels in female bipolar disorder PBMCs as tentative biomarker for distinct patient sub-phenotypes. Drug Dev Res 2019; 80:1128-1135. [PMID: 31498915 DOI: 10.1002/ddr.21598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 01/12/2023]
Abstract
Bipolar disorder (BD) is a complex neuropsychiatric disorder characterized by recurrent mania and depression episodes and requiring lifelong treatment with mood stabilizing drugs. Several lines of evidence, including with BD patient iPSC-derived neurons, suggest that neuronal hyperexcitability may underlie the key clinical symptoms of BD. Indeed, higher mRNA levels of SCN11A, coding for the voltage-gated sodium channel NaV 1.9 implicated in nociception, were detected in iPSC-derived neurons from BD patients, and were normalized by in vitro lithium. Here we studied SCN11A expression in peripheral blood mononuclear cells (PBMCs) from well-phenotyped female BD patients and controls and evaluated their association with several clinical sub-phenotypes. We observed higher mRNA levels of SCN11A in PBMCs from female BD patients with no records of alcohol dependence (p = .0050), no records of psychosis (p = .0097), or no records of suicide attempts (p = .0409). A trend was observed for higher SCN11A expression (FD = 1.91; p = .052) in BD PBMCs compared with controls. Datamining of published postmortem gene expression datasets indicated higher SCN11A expression in dorsolateral prefrontal cortex and orbitofrontal cortex tissues from BD patients compared with controls. Higher phenotype-associated expression levels in PBMC from BD patients were also observed for ID2 (alcohol dependence, suicide attempts) and HDGFRP3 (seasonal BD pattern). Our findings suggest that higher PBMC SCN11A expression levels may be associated with certain behavioral BD sub-phenotypes, including lack of alcohol dependence and psychosis, among BD patients. The NaV 1.9 voltage-gated sodium channel thus deserves consideration as a tentative phenotype modifier in BD.
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Affiliation(s)
- Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Michael J McCarthy
- Department of Psychiatry, University of California San Diego, La Jolla, California.,VA San Diego Healthcare System, San Diego, California
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California San Diego, La Jolla, California
| | - John R Kelsoe
- Department of Psychiatry, University of California San Diego, La Jolla, California
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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50
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Bhusal A, Rahman MH, Lee WH, Bae YC, Lee IK, Suk K. Paradoxical role of lipocalin-2 in metabolic disorders and neurological complications. Biochem Pharmacol 2019; 169:113626. [PMID: 31476294 DOI: 10.1016/j.bcp.2019.113626] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023]
Abstract
Lipocalin-2 (LCN2), also known as 24p3 and neutrophil gelatinase-associated lipocalin (NGAL), is a 25-kDa secreted protein implicated in various metabolic and inflammatory diseases. Early studies suggest the protective function of LCN2 in which it acts as a bacteriostatic agent that competes with bacteria for iron-bound siderophores. However, both detrimental and beneficial roles of LCN2 have recently been documented in metabolic and neuroinflammatory diseases. Metabolic inflammation, as observed in diabetes and obesity, has been closely associated with the upregulation of LCN2 in blood plasma and several tissues in both humans and rodents, suggesting its pro-diabetic and pro-obesogenic role. On the contrary, other studies imply an anti-diabetic and anti-obesogenic role of LCN2 whereby a deficiency in the Lcn2 gene results in the impairment of insulin sensitivity and enhances the high-fat-diet-induced expansion of fat. A similar dual role of LCN2 has also been reported in various animal models for neurological disorders. In the midst of these mixed findings, there is no experimental evidence to explain why LCN2 shows such a contrasting role in the various studies. This debate needs to be resolved (or reconciled) and an integrated view on the topic is desirable. Herein, we attempt to address this issue by reviewing the recent findings on LCN2 in metabolic disorders and assess the potential cellular or molecular mechanisms underlying the dual role of LCN2. We further discuss the possibilities and challenges of targeting LCN2 as a potential therapeutic strategy for metabolic disorders and neurological complications.
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Affiliation(s)
- Anup Bhusal
- Department of Pharmacology, Brain Science & Engineering Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Department of Biomedical Science, BK21 PLUS KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Md Habibur Rahman
- Department of Pharmacology, Brain Science & Engineering Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Department of Biomedical Science, BK21 PLUS KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Yong Chul Bae
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu, Republic of Korea
| | - In-Kyu Lee
- Department of Internal Medicine, Division of Endocrinology and Metabolism, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science & Engineering Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Department of Biomedical Science, BK21 PLUS KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
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