Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection
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Andres-Terre, 2015, Integrated, multi-cohort analysis identifies conserved transcriptional signatures across multiple respiratory viruses, Immunity, 43, 1199, 10.1016/j.immuni.2015.11.003
Barrett, 2013, NCBI GEO: archive for functional genomics data sets--update, Nucleic Acids Res., 41, D991, 10.1093/nar/gks1193
Ben-Hur, 1995, Menopause is associated with a significant increase in blood monocyte number and a relative decrease in the expression of estrogen receptors in human peripheral monocytes, Am. J. Reprod. Immunol., 34, 363, 10.1111/j.1600-0897.1995.tb00965.x
Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. B Stat. Methodol., 57, 289, 10.1111/j.2517-6161.1995.tb02031.x
Berry, 2010, An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis, Nature, 466, 973, 10.1038/nature09247
Bhattacharya, 2018, ImmPort, toward repurposing of open access immunological assay data for translational and clinical research, Sci. Data, 5, 180015, 10.1038/sdata.2018.15
Bongen, 2018, KLRD1-expressing natural killer cells predict influenza susceptibility, Genome Med., 10, 45, 10.1186/s13073-018-0554-1
Bouman, 2004, Gender difference in the non-specific and specific immune response in humans, Am. J. Reprod. Immunol., 52, 19, 10.1111/j.1600-0897.2004.00177.x
Britanova, 2016, Dynamics of individual T cell repertoires: from cord blood to centenarians, J. Immunol., 196, 5005, 10.4049/jimmunol.1600005
Bucasas, 2011, Early patterns of gene expression correlate with the humoral immune response to influenza vaccination in humans, J. Infect. Dis., 203, 921, 10.1093/infdis/jiq156
Carli, 2015, Leukopenia, lymphopenia, and neutropenia in systemic lupus erythematosus: prevalence and clinical impact: a systematic literature review, Semin. Arthritis Rheum., 45, 190, 10.1016/j.semarthrit.2015.05.009
Carlson, 2016, org.Hs.eg.db: Genome wide annotation for Human, R package version 3.4.0
Carr, 2016, The cellular composition of the human immune system is shaped by age and cohabitation, Nat. Immunol., 17, 461, 10.1038/ni.3371
Carroll, 2001, Innate immunity in the etiopathology of autoimmunity, Nat. Immunol., 2, 1089, 10.1038/ni1201-1089
Chiche, 2014, Modular transcriptional repertoire analyses of adults with systemic lupus erythematosus reveal distinct type I and type II interferon signatures, Arthritis Rheumatol., 66, 1583, 10.1002/art.38628
Cook, 2011, Sex disparities in cancer mortality and survival, Cancer Epidemiol. Biomarkers Prev., 20, 1629, 10.1158/1055-9965.EPI-11-0246
de Jong, 2012, A gene co-expression network in whole blood of schizophrenia patients is independent of antipsychotic-use and enriched for brain-expressed genes, PLoS ONE, 7, e39498, 10.1371/journal.pone.0039498
Dorak, 2012, Gender differences in cancer susceptibility: an inadequately addressed issue, Front. Genet., 3, 268, 10.3389/fgene.2012.00268
Durinck, 2009, Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt, Nat. Protoc., 4, 1184, 10.1038/nprot.2009.97
Eady, 2005, Variation in gene expression profiles of peripheral blood mononuclear cells from healthy volunteers, Physiol. Genomics, 22, 402, 10.1152/physiolgenomics.00080.2005
Fisher, 1934
Fragiadakis, 2019, Variation of immune cell responses in humans reveals sex-specific coordinated signaling across cell types, bioRxiv
Furman, 2013, Apoptosis and other immune biomarkers predict influenza vaccine responsiveness, Mol. Syst. Biol., 9, 659, 10.1038/msb.2013.15
Furman, 2014, Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination, Proc. Natl. Acad. Sci. USA, 111, 869, 10.1073/pnas.1321060111
Groth, 2013, Clinical review: Klinefelter syndrome—a clinical update, J. Clin. Endocrinol. Metab., 98, 20, 10.1210/jc.2012-2382
Haynes, 2017, Empowering multi-cohort gene expression analysis to increase reproducibility, Pac. Symp. Biocomput., 22, 144
Hedges, 2001, The power of statistical tests in meta-analysis, Psychol. Methods, 6, 203, 10.1037/1082-989X.6.3.203
Heinzen, 2008, Tissue-specific genetic control of splicing: implications for the study of complex traits, PLoS Biol., 6, e1, 10.1371/journal.pbio.1000001
Hemani, 2014, Detection and replication of epistasis influencing transcription in humans, Nature, 508, 249, 10.1038/nature13005
Hoang, 2014, Patient-based transcriptome-wide analysis identify interferon and ubiquination pathways as potential predictors of influenza A disease severity, PLoS ONE, 9, e111640, 10.1371/journal.pone.0111640
Huang, 2015, Global transcriptome analysis of peripheral blood identifies the most significantly down-regulated genes associated with metabolism regulation in Klinefelter syndrome, Mol. Reprod. Dev., 82, 17, 10.1002/mrd.22438
Idaghdour, 2010, Geographical genomics of human leukocyte gene expression variation in southern Morocco, Nat. Genet., 42, 62, 10.1038/ng.495
Jansen, 2014, Sex differences in the human peripheral blood transcriptome, BMC Genomics, 15, 33, 10.1186/1471-2164-15-33
Khan, 2016, The immune system is a natural target for estrogen action: opposing effects of estrogen in two prototypical autoimmune diseases, Front. Immunol., 6, 635, 10.3389/fimmu.2015.00635
Khatri, 2013, A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation, J. Exp. Med., 210, 2205, 10.1084/jem.20122709
Klein, 2015, Sex-based differences in immune function and responses to vaccination, Trans. R. Soc. Trop. Med. Hyg., 109, 9, 10.1093/trstmh/tru167
Kuespert, 2006, CEACAMs: their role in physiology and pathophysiology, Curr. Opin. Cell Biol., 18, 565, 10.1016/j.ceb.2006.08.008
Kuparinen, 2013, Cytomegalovirus (CMV)-dependent and -independent changes in the aging of the human immune system: a transcriptomic analysis, Exp. Gerontol., 48, 305, 10.1016/j.exger.2012.12.010
Lauwerys, 2013, Down-regulation of interferon signature in systemic lupus erythematosus patients by active immunization with interferon α-kinoid, Arthritis Rheum., 65, 447, 10.1002/art.37785
Lewis, 2011, Whole blood gene expression analyses in patients with single versus recurrent venous thromboembolism, Thromb. Res., 128, 536, 10.1016/j.thromres.2011.06.003
Liang, 2017, A gene network regulated by the transcription factor VGLL3 as a promoter of sex-biased autoimmune diseases, Nat. Immunol., 18, 152, 10.1038/ni.3643
Libert, 2010, The X chromosome in immune functions: when a chromosome makes the difference, Nat. Rev. Immunol., 10, 594, 10.1038/nri2815
Liu, 2016, An individualized predictor of health and disease using paired reference and target samples, BMC Bioinformatics, 17, 47, 10.1186/s12859-016-0889-9
Lorenzo, 2011, Antibody responses and cross protection against lethal influenza A viruses differ between the sexes in C57BL/6 mice, Vaccine, 29, 9246, 10.1016/j.vaccine.2011.09.110
Lugada, 2004, Population-based hematologic and immunologic reference values for a healthy Ugandan population, Clin. Diagn. Lab. Immunol., 11, 29
Mason, 2010, Maternal influences on the transmission of leukocyte gene expression profiles in population samples from Brisbane, Australia, PLoS ONE, 5, e14479, 10.1371/journal.pone.0014479
McHale, 2011, Global gene expression profiling of a population exposed to a range of benzene levels, Environ. Health Perspect., 119, 628, 10.1289/ehp.1002546
Melé, 2015, Human genomics. The human transcriptome across tissues and individuals, Science, 348, 660, 10.1126/science.aaa0355
Melzer, 2015, Reference intervals for leukocyte subsets in adults: Results from a population-based study using 10-color flow cytometry, Cytometry B Clin. Cytom., 88, 270, 10.1002/cyto.b.21234
Moraes, 2006, Neutrophil granule contents in the pathogenesis of lung injury, Curr. Opin. Hematol., 13, 21, 10.1097/01.moh.0000190113.31027.d5
Newman, 2015, Robust enumeration of cell subsets from tissue expression profiles, Nat. Methods, 12, 453, 10.1038/nmeth.3337
Owens, 2002, Ecology and evolution. Sex differences in mortality rate, Science, 297, 2008, 10.1126/science.1076813
Patin, 2018, Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors, Nat. Immunol., 19, 302, 10.1038/s41590-018-0049-7
Peters, 2015, The transcriptional landscape of age in human peripheral blood, Nat. Commun., 6, 8570, 10.1038/ncomms9570
Piasecka, 2018, Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges, Proc. Natl. Acad. Sci. USA, 115, E488, 10.1073/pnas.1714765115
Querec, 2009, Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans, Nat. Immunol., 10, 116, 10.1038/ni.1688
Ramasamy, 2008, Key issues in conducting a meta-analysis of gene expression microarray datasets, PLoS Med., 5, e184, 10.1371/journal.pmed.0050184
Rojas-Pena, 2018, Profiling gene expression of the host response to a Plasmodium vivax irradiated sporozoite immunization and infectious challenge, bioRxiv
Roy Chowdhury, 2018, A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes, Nature, 560, 644, 10.1038/s41586-018-0439-x
Sammaritano, 2012, Menopause in patients with autoimmune diseases, Autoimmun. Rev., 11, A430, 10.1016/j.autrev.2011.11.006
Sasidhar, 2012, The XX sex chromosome complement in mice is associated with increased spontaneous lupus compared with XY, Ann. Rheum. Dis., 71, 1418, 10.1136/annrheumdis-2011-201246
Schultz, 2007, The bactericidal/permeability-increasing protein (BPI) in infection and inflammatory disease, Clin. Chim. Acta, 384, 12, 10.1016/j.cca.2007.07.005
Scott, 2019, Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study, Lancet Respir. Med., 7, 497, 10.1016/S2213-2600(18)30508-3
Seidler, 2010, Age-dependent alterations of monocyte subsets and monocyte-related chemokine pathways in healthy adults, BMC Immunol., 11, 30, 10.1186/1471-2172-11-30
Seok, 2013, Genomic responses in mouse models poorly mimic human inflammatory diseases, Proc. Natl. Acad. Sci. USA, 110, 3507, 10.1073/pnas.1222878110
Shen-Orr, 2016, Defective signaling in the JAK-STAT pathway tracks with chronic inflammation and cardiovascular risk in aging humans, Cell Syst., 3, 374, 10.1016/j.cels.2016.09.009
Souyris, 2018, TLR7 escapes X chromosome inactivation in immune cells, Sci. Immunol., 3, 3, 10.1126/sciimmunol.aap8855
Toker, 2016, Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies, F1000Res., 5, 2103, 10.12688/f1000research.9471.1
Tsang, 2014, Global analyses of human immune variation reveal baseline predictors of postvaccination responses, Cell, 157, 499, 10.1016/j.cell.2014.03.031
Tukiainen, 2017, Landscape of X chromosome inactivation across human tissues, Nature, 550, 244, 10.1038/nature24265
Vahey, 2010, Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine, J. Infect. Dis., 201, 580, 10.1086/650310
Vallania, 2018, Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases, Nat. Commun., 9, 4735, 10.1038/s41467-018-07242-6
Vedhara, 2015, Personality and gene expression: Do individual differences exist in the leukocyte transcriptome?, Psychoneuroendocrinology, 52, 72, 10.1016/j.psyneuen.2014.10.028
Vermillion, 2018, Production of amphiregulin and recovery from influenza is greater in males than females, Biol. Sex Differ., 9, 24, 10.1186/s13293-018-0184-8
Whitney, 2003, Individuality and variation in gene expression patterns in human blood, Proc. Natl. Acad. Sci. USA, 100, 1896, 10.1073/pnas.252784499
Zhai, 2015, Host transcriptional response to influenza and other acute respiratory viral infections: a prospective cohort study, PLoS Pathog., 11, e1004869, 10.1371/journal.ppat.1004869