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Chin IM, Gardell ZA, Corces MR. Decoding polygenic diseases: advances in noncoding variant prioritization and validation. Trends Cell Biol 2024; 34:465-483. [PMID: 38719704 DOI: 10.1016/j.tcb.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/12/2024] [Accepted: 03/21/2024] [Indexed: 06/09/2024]
Abstract
Genome-wide association studies (GWASs) provide a key foundation for elucidating the genetic underpinnings of common polygenic diseases. However, these studies have limitations in their ability to assign causality to particular genetic variants, especially those residing in the noncoding genome. Over the past decade, technological and methodological advances in both analytical and empirical prioritization of noncoding variants have enabled the identification of causative variants by leveraging orthogonal functional evidence at increasing scale. In this review, we present an overview of these approaches and describe how this workflow provides the groundwork necessary to move beyond associations toward genetically informed studies on the molecular and cellular mechanisms of polygenic disease.
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Affiliation(s)
- Iris M Chin
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Zachary A Gardell
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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2
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Quiros-Roldan E, Sottini A, Natali PG, Imberti L. The Impact of Immune System Aging on Infectious Diseases. Microorganisms 2024; 12:775. [PMID: 38674719 PMCID: PMC11051847 DOI: 10.3390/microorganisms12040775] [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: 03/01/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Immune system aging is becoming a field of increasing public health interest because of prolonged life expectancy, which is not paralleled by an increase in health expectancy. As age progresses, innate and adaptive immune systems undergo changes, which are defined, respectively, as inflammaging and immune senescence. A wealth of available data demonstrates that these two conditions are closely linked, leading to a greater vulnerability of elderly subjects to viral, bacterial, and opportunistic infections as well as lower post-vaccination protection. To face this novel scenario, an in-depth assessment of the immune players involved in this changing epidemiology is demanded regarding the individual and concerted involvement of immune cells and mediators within endogenous and exogenous factors and co-morbidities. This review provides an overall updated description of the changes affecting the aging immune system, which may be of help in understanding the underlying mechanisms associated with the main age-associated infectious diseases.
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Affiliation(s)
- Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, ASST- Spedali Civili and DSCS- University of Brescia, 25123 Brescia, Italy;
| | - Alessandra Sottini
- Clinical Chemistry Laboratory, Services Department, ASST Spedali Civili of Brescia, 25123 Brescia, Italy;
| | - Pier Giorgio Natali
- Mediterranean Task Force for Cancer Control (MTCC), Via Pizzo Bernina, 14, 00141 Rome, Italy;
| | - Luisa Imberti
- Section of Microbiology, University of Brescia, P. le Spedali Civili, 1, 25123 Brescia, Italy
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3
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Roussos P, Ma Y, Girdhar K, Hoffman G, Fullard J, Bendl J. Sex differences in brain cell-type specific chromatin accessibility in schizophrenia. RESEARCH SQUARE 2024:rs.3.rs-4158509. [PMID: 38645177 PMCID: PMC11030506 DOI: 10.21203/rs.3.rs-4158509/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Our understanding of the sex-specific role of the non-coding genome in serious mental illness remains largely incomplete. To address this gap, we explored sex differences in 1,393 chromatin accessibility profiles, derived from neuronal and non-neuronal nuclei of two distinct cortical regions from 234 cases with serious mental illness and 235 controls. We identified sex-specific enhancer-promoter interactions and showed that they regulate genes involved in X-chromosome inactivation (XCI). Examining chromosomal conformation allowed us to identify sex-specific cis- and trans-regulatory domains (CRDs and TRDs). Co-localization of sex-specific TRDs with schizophrenia common risk variants pinpointed male-specific regulatory regions controlling a number of metabolic pathways. Additionally, enhancers from female-specific TRDs were found to regulate two genes known to escape XCI, (XIST and JPX), underlying the importance of TRDs in deciphering sex differences in schizophrenia. Overall, these findings provide extensive characterization of sex differences in the brain epigenome and disease-associated regulomes.
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Affiliation(s)
| | - Yixuan Ma
- Icahn School of Medicine at Mount Sinai
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Peeters SB, Posynick BJ, Brown CJ. Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation. EPIGENOMES 2023; 7:29. [PMID: 38131901 PMCID: PMC10742877 DOI: 10.3390/epigenomes7040029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome-in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact.
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Affiliation(s)
| | | | - Carolyn J. Brown
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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5
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Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [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] [Indexed: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
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Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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6
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Pratt HE, Wu T, Elhajjajy S, Zhou J, Fitzgerald K, Fazzio T, Weng Z, Pratt DS. Beyond genome-wide association studies: Investigating the role of noncoding regulatory elements in primary sclerosing cholangitis. Hepatol Commun 2023; 7:e0242. [PMID: 37756045 PMCID: PMC10531193 DOI: 10.1097/hc9.0000000000000242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified 30 risk loci for primary sclerosing cholangitis (PSC). Variants within these loci are found predominantly in noncoding regions of DNA making their mechanisms of conferring risk hard to define. Epigenomic studies have shown noncoding variants broadly impact regulatory element activity. The possible association of noncoding PSC variants with regulatory element activity has not been studied. We aimed to (1) determine if the noncoding risk variants in PSC impact regulatory element function and (2) if so, assess the role these regulatory elements have in explaining the genetic risk for PSC. METHODS Available epigenomic datasets were integrated to build a comprehensive atlas of cell type-specific regulatory elements, emphasizing PSC-relevant cell types. RNA-seq and ATAC-seq were performed on peripheral CD4+ T cells from 10 PSC patients and 11 healthy controls. Computational techniques were used to (1) study the enrichment of PSC-risk variants within regulatory elements, (2) correlate risk genotype with differences in regulatory element activity, and (3) identify regulatory elements differentially active and genes differentially expressed between PSC patients and controls. RESULTS Noncoding PSC-risk variants are strongly enriched within immune-specific enhancers, particularly ones involved in T-cell response to antigenic stimulation. In total, 250 genes and >10,000 regulatory elements were identified that are differentially active between patients and controls. CONCLUSIONS Mechanistic effects are proposed for variants at 6 PSC-risk loci where genotype was linked with differential T-cell regulatory element activity. Regulatory elements are shown to play a key role in PSC pathophysiology.
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Affiliation(s)
- Henry E. Pratt
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Tong Wu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Shaimae Elhajjajy
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeffrey Zhou
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical, School, Worcester, Massachusetts, USA
| | - Kate Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical, School, Worcester, Massachusetts, USA
| | - Tom Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Daniel S. Pratt
- Autoimmune & Cholestatic Liver Center, GI Division, Massachusetts General Hospital, Boston, Massachusetts, USA
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7
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Singh PP, Benayoun BA. Considerations for reproducible omics in aging research. NATURE AGING 2023; 3:921-930. [PMID: 37386258 PMCID: PMC10527412 DOI: 10.1038/s43587-023-00448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
Technical advancements over the past two decades have enabled the measurement of the panoply of molecules of cells and tissues including transcriptomes, epigenomes, metabolomes and proteomes at unprecedented resolution. Unbiased profiling of these molecular landscapes in the context of aging can reveal important details about mechanisms underlying age-related functional decline and age-related diseases. However, the high-throughput nature of these experiments creates unique analytical and design demands for robustness and reproducibility. In addition, 'omic' experiments are generally onerous, making it crucial to effectively design them to eliminate as many spurious sources of variation as possible as well as account for any biological or technical parameter that may influence such measures. In this Perspective, we provide general guidelines on best practices in the design and analysis of omic experiments in aging research from experimental design to data analysis and considerations for long-term reproducibility and validation of such studies.
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Affiliation(s)
- Param Priya Singh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, USA.
- Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
- USC Stem Cell Initiative, Los Angeles, CA, USA.
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8
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Krueger K, Lamenza F, Gu H, El-Hodiri H, Wester J, Oberdick J, Fischer AJ, Oghumu S. Sex differences in susceptibility to substance use disorder: Role for X chromosome inactivation and escape? Mol Cell Neurosci 2023; 125:103859. [PMID: 37207894 PMCID: PMC10286730 DOI: 10.1016/j.mcn.2023.103859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
There is a sex-based disparity associated with substance use disorders (SUDs) as demonstrated by clinical and preclinical studies. Females are known to escalate from initial drug use to compulsive drug-taking behavior (telescoping) more rapidly, and experience greater negative withdrawal effects than males. Although these biological differences have largely been attributed to sex hormones, there is evidence for non-hormonal factors, such as the influence of the sex chromosome, which underlie sex disparities in addiction behavior. However, genetic and epigenetic mechanisms underlying sex chromosome influences on substance abuse behavior are not completely understood. In this review, we discuss the role that escape from X-chromosome inactivation (XCI) in females plays in sex-associated differences in addiction behavior. Females have two X chromosomes (XX), and during XCI, one X chromosome is randomly chosen to be transcriptionally silenced. However, some X-linked genes escape XCI and display biallelic gene expression. We generated a mouse model using an X-linked gene specific bicistronic dual reporter mouse as a tool to visualize allelic usage and measure XCI escape in a cell specific manner. Our results revealed a previously undiscovered X-linked gene XCI escaper (CXCR3), which is variable and cell type dependent. This illustrates the highly complex and context dependent nature of XCI escape which is largely understudied in the context of SUD. Novel approaches such as single cell RNA sequencing will provide a global molecular landscape and impact of XCI escape in addiction and facilitate our understanding of the contribution of XCI escape to sex disparities in SUD.
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Affiliation(s)
- Kate Krueger
- Department of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Felipe Lamenza
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Howard Gu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Heithem El-Hodiri
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Jason Wester
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - John Oberdick
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Andy J Fischer
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | - Steve Oghumu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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9
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Gong W, Dsouza N, Garry DJ. SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors. Genome Biol 2023; 24:125. [PMID: 37218013 DOI: 10.1186/s13059-023-02954-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor-induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data.
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Affiliation(s)
- Wuming Gong
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
| | - Nikita Dsouza
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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10
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Watanabe M, Motooka D, Yamasaki S. The kinetics of signaling through the common FcRγ chain determine cytokine profiles in dendritic cells. Sci Signal 2023; 16:eabn9909. [PMID: 36881655 DOI: 10.1126/scisignal.abn9909] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The common Fc receptor γ (FcRγ) chain is a signaling subunit common to several immune receptors, but cellular responses induced by FcRγ-coupled receptors are diverse. We investigated the mechanisms by which FcRγ generates divergent signals when coupled to Dectin-2 and Mincle, structurally similar C-type lectin receptors that induce the release of different cytokines from dendritic cells. Chronological tracing of transcriptomic and epigenetic changes upon stimulation revealed that Dectin-2 induced early and strong signaling, whereas Mincle-mediated signaling was delayed, which reflects their expression patterns. Generation of early and strong FcRγ-Syk signaling by engineered chimeric receptors was sufficient to recapitulate a Dectin-2-like gene expression profile. Early Syk signaling selectively stimulated the activity of the calcium ion-activated transcription factor NFAT, which rapidly altered the chromatin status and transcription of the Il2 gene. In contrast, proinflammatory cytokines, such as TNF, were induced regardless of FcRγ signaling kinetics. These results suggest that the strength and timing of FcRγ-Syk signaling can alter the quality of cellular responses through kinetics-sensing signaling machineries.
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Affiliation(s)
- Miyuki Watanabe
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka 565-0871, Japan.,Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.,Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
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11
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A roadmap for translational cancer glycoimmunology at single cell resolution. J Exp Clin Cancer Res 2022; 41:143. [PMID: 35428302 PMCID: PMC9013178 DOI: 10.1186/s13046-022-02335-z] [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: 02/03/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022] Open
Abstract
Cancer cells can evade immune responses by exploiting inhibitory immune checkpoints. Immune checkpoint inhibitor (ICI) therapies based on anti-CTLA-4 and anti-PD-1/PD-L1 antibodies have been extensively explored over the recent years to unleash otherwise compromised anti-cancer immune responses. However, it is also well established that immune suppression is a multifactorial process involving an intricate crosstalk between cancer cells and the immune systems. The cancer glycome is emerging as a relevant source of immune checkpoints governing immunosuppressive behaviour in immune cells, paving an avenue for novel immunotherapeutic options. This review addresses the current state-of-the-art concerning the role played by glycans controlling innate and adaptive immune responses, while shedding light on available experimental models for glycoimmunology. We also emphasize the tremendous progress observed in the development of humanized models for immunology, the paramount contribution of advances in high-throughput single-cell analysis in this context, and the importance of including predictive machine learning algorithms in translational research. This may constitute an important roadmap for glycoimmunology, supporting careful adoption of models foreseeing clinical translation of fundamental glycobiology knowledge towards next generation immunotherapies.
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12
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Hayes LN, An K, Carloni E, Li F, Vincent E, Trippaers C, Paranjpe M, Dölen G, Goff LA, Ramos A, Kano SI, Sawa A. Prenatal immune stress blunts microglia reactivity, impairing neurocircuitry. Nature 2022; 610:327-334. [PMID: 36171283 DOI: 10.1038/s41586-022-05274-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/24/2022] [Indexed: 01/12/2023]
Abstract
Recent studies suggested that microglia, the primary brain immune cells, can affect circuit connectivity and neuronal function1,2. Microglia infiltrate the neuroepithelium early in embryonic development and are maintained in the brain throughout adulthood3,4. Several maternal environmental factors-such as an aberrant microbiome, immune activation and poor nutrition-can influence prenatal brain development5,6. Nevertheless, it is unknown how changes in the prenatal environment instruct the developmental trajectory of infiltrating microglia, which in turn affect brain development and function. Here we show that, after maternal immune activation (MIA) in mice, microglia from the offspring have a long-lived decrease in immune reactivity (blunting) across the developmental trajectory. The blunted immune response was accompanied by changes in chromatin accessibility and reduced transcription factor occupancy of the open chromatin. Single-cell RNA-sequencing analysis revealed that MIA does not induce a distinct subpopulation but, rather, decreases the contribution to inflammatory microglia states. Prenatal replacement of microglia from MIA offspring with physiological infiltration of naive microglia ameliorated the immune blunting and restored a decrease in presynaptic vesicle release probability onto dopamine receptor type-two medium spiny neurons, indicating that aberrantly formed microglia due to an adverse prenatal environment affect the long-term microglia reactivity and proper striatal circuit development.
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Affiliation(s)
- Lindsay N Hayes
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyongman An
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elisa Carloni
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fangze Li
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Vincent
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chloë Trippaers
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - Manish Paranjpe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gül Dölen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adriana Ramos
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shin-Ichi Kano
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Akira Sawa
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Mental Health, Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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13
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Pujantell M, Altfeld M. Consequences of sex differences in Type I IFN responses for the regulation of antiviral immunity. Front Immunol 2022; 13:986840. [PMID: 36189206 PMCID: PMC9522975 DOI: 10.3389/fimmu.2022.986840] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
The immune system protects us from pathogens, such as viruses. Antiviral immune mechanisms aim to limit viral replication, and must maintain immunological homeostasis to avoid excessive inflammation and damage to the host. Sex differences in the manifestation and progression of immune-mediated disease point to sex-specific factors modulating antiviral immunity. The exact mechanisms regulating these immunological differences between females and males are still insufficiently understood. Females are known to display stronger Type I IFN responses and are less susceptible to viral infections compared to males, indicating that Type I IFN responses might contribute to the sexual dimorphisms observed in antiviral responses. Here, we review the impact of sex hormones and X chromosome-encoded genes on differences in Type I IFN responses between females and males; and discuss the consequences of sex differences in Type I IFN responses for the regulation of antiviral immune responses.
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14
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Zhang Z, Zhang Y, Bao Q, Gu Y, Liang C, Chu M, Guo X, Bao P, Yan P. The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation. Int J Mol Sci 2022; 23:ijms23179960. [PMID: 36077381 PMCID: PMC9456067 DOI: 10.3390/ijms23179960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
Although significant advancement has been made in the study of adipogenesis, knowledge about how chromatin accessibility regulates yak adipogenesis is lacking. We here described genome-wide dynamic chromatin accessibility in preadipocytes and adipocytes by using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and thus revealed the unique characteristics of open chromatin during yak adipocyte differentiation. The chromatin accessibility of preadipocytes and adipocytes exhibited a similar genomic distribution, displaying a preferential location within the intergenic region, intron, and promoter. The pathway enrichment analysis identified that genes with differential chromatin accessibility were involved in adipogenic metabolism regulation pathways, such as the peroxisome proliferator activated receptor-γ (PPAR) signaling pathway, wingless-type MMTV integration site (Wnt) signaling pathway, and extracellular matrix-receptor (ECM–receptor) interaction. Integration of ATAC-seq and mRNA-seq revealed that genes with a high expression were associated with high levels of chromatin accessibility, especially within 1 kb upstream and downstream of the transcription start site. In addition, we identified a series of transcription factors (TFs) related to adipogenesis and created the TF regulatory network, providing the possible interactions between TFs during yak adipogenesis. This study is crucial for advancing the understanding of transcriptional regulatory mechanisms of adipogenesis and provides valuable information for understanding the adaptation of plateau species to high-altitude environments by maintaining whole body homeostasis through fat metabolism.
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Affiliation(s)
- Zhilong Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yongfeng Zhang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Qi Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yarong Gu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-931-216-4180
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15
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Peckham H, Webb K, Rosser EC, Butler G, Ciurtin C. Gender-Diverse Inclusion in Immunological Research: Benefits to Science and Health. Front Med (Lausanne) 2022; 9:909789. [PMID: 35911383 PMCID: PMC9329564 DOI: 10.3389/fmed.2022.909789] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/24/2022] [Indexed: 01/26/2023] Open
Abstract
The differences between male and female immune systems are an under-researched field, ripe for discovery. This is evidenced by the stark sex biases seen in autoimmunity and infectious disease. Both the sex hormones (oestrogen and testosterone), as well as the sex chromosomes have been demonstrated to impact immune responses, in multiple ways. Historical shortcomings in reporting basic and clinical scientific findings in a sex-disaggregated manner have led not only to limited discovery of disease aetiology, but to potential inaccuracies in the estimation of the effects of diseases or interventions on females and gender-diverse groups. Here we propose not only that research subjects should include both cis-gender men and cis-gender women, but also transgender and gender-diverse people alongside them. The known interaction between the hormonal milieu and the sex chromosomes is inseparable in cis-gender human research, without the confounders of puberty and age. By inclusion of those pursuing hormonal affirmation of their gender identity- the individual and interactive investigation of hormones and chromosomes is permitted. Not only does this allow for a fine-tuned dissection of these individual effects, but it allows for discovery that is both pertinent and relevant to a far wider portion of the population. There is an unmet need for detailed treatment follow-up of the transgender community- little is known of the potential benefits and risks of hormonal supplementation on the immune system, nor indeed on many other health and disease outcomes. Our research team has pioneered the inclusion of gender-diverse persons in our basic research in adolescent autoimmune rheumatic diseases. We review here the many avenues that remain unexplored, and suggest ways in which other groups and teams can broaden their horizons and invest in a future for medicine that is both fruitful and inclusive.
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Affiliation(s)
- Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospital (UCLH), Great Ormond Street Hospital (GOSH), London, United Kingdom,Division of Medicine, Centre for Rheumatology Research, University College London (UCL), London, United Kingdom,*Correspondence: Hannah Peckham,
| | - Kate Webb
- Department of Paediatric Rheumatology, School of Child and Adolescent Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Cape Town, South Africa,Crick African Network, The Francis Crick Institute, London, United Kingdom
| | - Elizabeth C. Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospital (UCLH), Great Ormond Street Hospital (GOSH), London, United Kingdom,Division of Medicine, Centre for Rheumatology Research, University College London (UCL), London, United Kingdom
| | - Gary Butler
- Department of Paediatric and Adolescent Endocrinology, University College London Hospital (UCLH) and Great Ormond Street Institute of Child Health, University College London, London, United Kingdom,Gender Identity Development Service (GIDS), Tavistock and Portman NHS Foundation Trust, London, United Kingdom
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at University College London (UCL), University College London Hospital (UCLH), Great Ormond Street Hospital (GOSH), London, United Kingdom,Division of Medicine, Centre for Rheumatology Research, University College London (UCL), London, United Kingdom
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16
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Liu N, Sadlon T, Wong YY, Pederson S, Breen J, Barry SC. 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk. Epigenetics Chromatin 2022; 15:24. [PMID: 35773720 PMCID: PMC9244893 DOI: 10.1186/s13072-022-00456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have enabled the discovery of single nucleotide polymorphisms (SNPs) that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the identified variants lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression. To address this problem, we developed a variant filtering workflow called 3DFAACTS-SNP to link genetic variants to target genes in a cell-specific manner. Here, we use 3DFAACTS-SNP to identify candidate SNPs and target genes associated with the loss of immune tolerance in regulatory T cells (Treg) in T1D. Results Using 3DFAACTS-SNP, we identified from a list of 1228 previously fine-mapped variants, 36 SNPs with plausible Treg-specific mechanisms of action. The integration of cell type-specific chromosome conformation capture data in 3DFAACTS-SNP identified 266 regulatory regions and 47 candidate target genes that interact with these variant-containing regions in Treg cells. We further demonstrated the utility of the workflow by applying it to three other SNP autoimmune datasets, identifying 16 Treg-centric candidate variants and 60 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of all known common (> 10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 9376 candidate variants and 4968 candidate target genes, generating a list of potential sites for future T1D or other autoimmune disease research. Conclusions We demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function, and illustrate the power of using cell type-specific multi-omics datasets to determine disease mechanisms. Our workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00456-5.
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Affiliation(s)
- Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Stephen Pederson
- Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, Australia. .,Robinson Research Institute, University of Adelaide, Adelaide, Australia. .,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia. .,Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia. .,John Curtin School of Medical Research, Australian National University, Canberra, Australia.
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
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17
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Jiwrajka N, Anguera MC. The X in seX-biased immunity and autoimmune rheumatic disease. J Exp Med 2022; 219:e20211487. [PMID: 35510951 PMCID: PMC9075790 DOI: 10.1084/jem.20211487] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/04/2022] [Accepted: 03/31/2022] [Indexed: 01/07/2023] Open
Abstract
Sexual dimorphism in the composition and function of the human immune system has important clinical implications, as males and females differ in their susceptibility to infectious diseases, cancers, and especially systemic autoimmune rheumatic diseases. Both sex hormones and the X chromosome, which bears a number of immune-related genes, play critical roles in establishing the molecular basis for the observed sex differences in immune function and dysfunction. Here, we review our current understanding of sex differences in immune composition and function in health and disease, with a specific focus on the contribution of the X chromosome to the striking female bias of three autoimmune rheumatic diseases.
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Affiliation(s)
- Nikhil Jiwrajka
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Montserrat C. Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
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18
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Ho JQ, Sepand MR, Bigdelou B, Shekarian T, Esfandyarpour R, Chauhan P, Serpooshan V, Beura LK, Hutter G, Zanganeh S. The immune response to COVID-19: Does sex matter? Immunology 2022; 166:429-443. [PMID: 35470422 PMCID: PMC9111683 DOI: 10.1111/imm.13487] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/14/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID‐19) pandemic has created unprecedented challenges worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes COVID‐19 and has a complex interaction with the immune system, including growing evidence of sex‐specific differences in the immune response. Sex‐disaggregated analyses of epidemiological data indicate that males experience more severe symptoms and suffer higher mortality from COVID‐19 than females. Many behavioural risk factors and biological factors may contribute to the different immune response. This review examines the immune response to SARS‐CoV‐2 infection in the context of sex, with emphasis on potential biological mechanisms explaining differences in clinical outcomes. Understanding sex differences in the pathophysiology of SARS‐CoV‐2 infection will help promote the development of specific strategies to manage the disease.
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Affiliation(s)
- Jim Q Ho
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States
| | - Mohammad Reza Sepand
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, United States
| | - Banafsheh Bigdelou
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, United States
| | - Tala Shekarian
- Department of Neurosurgery, University Hospital Basel, Basel, Switzerland
| | - Rahim Esfandyarpour
- Department of Electrical Engineering, University of California Irvine, Irvine, California, United States.,Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States
| | - Prashant Chauhan
- Laboratory of Functional Biology of Protists, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Vahid Serpooshan
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine and Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Lalit K Beura
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, United States
| | - Gregor Hutter
- Department of Neurosurgery, University Hospital Basel, Basel, Switzerland
| | - Steven Zanganeh
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, United States
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19
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Giles JR, Manne S, Freilich E, Oldridge DA, Baxter AE, George S, Chen Z, Huang H, Chilukuri L, Carberry M, Giles L, Weng NPP, Young RM, June CH, Schuchter LM, Amaravadi RK, Xu X, Karakousis GC, Mitchell TC, Huang AC, Shi J, Wherry EJ. Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers. Immunity 2022; 55:557-574.e7. [PMID: 35263570 PMCID: PMC9214622 DOI: 10.1016/j.immuni.2022.02.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/27/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022]
Abstract
The clinical benefit of T cell immunotherapies remains limited by incomplete understanding of T cell differentiation and dysfunction. We generated an epigenetic and transcriptional atlas of T cell differentiation from healthy humans that included exhausted CD8 T cells and applied this resource in three ways. First, we identified modules of gene expression and chromatin accessibility, revealing molecular coordination of differentiation after activation and between central memory and effector memory. Second, we applied this healthy molecular framework to three settings-a neoadjuvant anti-PD1 melanoma trial, a basal cell carcinoma scATAC-seq dataset, and autoimmune disease-associated SNPs-yielding insights into disease-specific biology. Third, we predicted genome-wide cis-regulatory elements and validated this approach for key effector genes using CRISPR interference, providing functional annotation and demonstrating the ability to identify targets for non-coding cellular engineering. These studies define epigenetic and transcriptional regulation of human T cells and illustrate the utility of interrogating disease in the context of a healthy T cell atlas.
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Affiliation(s)
- Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Freilich
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Derek A Oldridge
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sangeeth George
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hua Huang
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Lakshmi Chilukuri
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Mary Carberry
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lydia Giles
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nan-Ping P Weng
- Laboratory of Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Regina M Young
- Center for Cellular Immunotherapies, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carl H June
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lynn M Schuchter
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi K Amaravadi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giorgos C Karakousis
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tara C Mitchell
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Junwei Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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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: 21] [Impact Index Per Article: 10.5] [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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21
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Orozco G. Fine mapping with epigenetic information and 3D structure. Semin Immunopathol 2022; 44:115-125. [PMID: 35022890 PMCID: PMC8837508 DOI: 10.1007/s00281-021-00906-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022]
Abstract
Since 2005, thousands of genome-wide association studies (GWAS) have been published, identifying hundreds of thousands of genetic variants that increase risk of complex traits such as autoimmune diseases. This wealth of data has the potential to improve patient care, through personalized medicine and the identification of novel drug targets. However, the potential of GWAS for clinical translation has not been fully achieved yet, due to the fact that the functional interpretation of risk variants and the identification of causal variants and genes are challenging. The past decade has seen the development of great advances that are facilitating the overcoming of these limitations, by utilizing a plethora of genomics and epigenomics tools to map and characterize regulatory elements and chromatin interactions, which can be used to fine map GWAS loci, and advance our understanding of the biological mechanisms that cause disease.
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Affiliation(s)
- Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9LJ, UK. .,NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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22
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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23
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Pinto JA, Araujo JM, Gómez HL. Sex, immunity, and cancer. Biochim Biophys Acta Rev Cancer 2021; 1877:188647. [PMID: 34767966 DOI: 10.1016/j.bbcan.2021.188647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023]
Abstract
The composition of the tumor microenvironment is the complex result of the interaction between tumoral and host factors. Since there are several differences in the regulation of gene circuits between sexes, mainly influenced by sex hormones, the tumor-host interaction presents some differences, leading tumors to evolve under different conditions. Nowadays, it is well known the existence of sexual dimorphism in the regulation of the immune system, where women present an improved immunity to various infectious agents and, on the other hand, a higher incidence of autoimmune diseases than men. In oncology, differences in cancer susceptibility, response to treatment, and clinical outcomes between men and women patients are well known. Recently, sex-specific differences have also been reported in mutations in driver genes and the prognostic value of several biomarkers. Sex has been a widely forgotten biomarker in cancer therapy, but it has recently acquired great relevance due to the different results seen in immunotherapy treatment.
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Affiliation(s)
- Joseph A Pinto
- Escuela de Medicina Humana-Filial Ica, Universidad Privada San Juan Bautista, Panamericana Sur Km. 305, 11004 Ica, Peru.
| | - Jhajaira M Araujo
- Centro de Investigación Básica y Traslacional, AUNA-Ideas, Guardia Civil 571, San Borja, Lima 41, Peru
| | - Henry L Gómez
- Departamento de Medicina Oncológica, Instituto Nacional de Enfermedades Neoplásicas, Av. Angamos Este 2520, Surquillo, Lima 34, Peru
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24
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Araujo JM, Rosas G, Belmar-López C, Raez LE, Rolfo CD, Schwarz LJ, Infante-Huaytalla U, Paez KJ, García LR, Alvarado H, Ramos FP, Delgado-Espinoza SS, Cardenas-Farfan JB, Cornejo M, Zanabria D, Colonio-Cossio C, Rojas-Jefferson M, Pinto JA. Influence of Sex in the Molecular Characteristics and Outcomes of Malignant Tumors. Front Oncol 2021; 11:752918. [PMID: 34737960 PMCID: PMC8562721 DOI: 10.3389/fonc.2021.752918] [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] [Received: 08/03/2021] [Accepted: 09/29/2021] [Indexed: 01/22/2023] Open
Abstract
Background Sex is frequently underestimated as a prognostic biomarker in cancer. In this study, we evaluated a large cohort of patients and public datasets to determine the influence of sex on clinical outcomes, mutational status, and activation of immune pathways in different types of cancer. Methods A cohort of 13,619 Oncosalud-affiliated patients bearing sex-unrelated cancers was followed over a 20-year period. Hazard ratios (HRs) for death were estimated for female vs. male patients for each cancer type and then pooled in a meta-analysis to obtain an overall HR. In addition, the mutational status of the main actionable genes in melanoma (MEL), colorectal cancer (CRC), and lung cancer was compared between sexes. Finally, a gene set enrichment analysis (GSEA) of publicly available data was conducted, to assess differences in immune processes between sexes in MEL, gastric adenocarcinoma (GC), head and neck cancer (HNC), colon cancer (CC), liver cancer (LC), pancreatic cancer (PC), thyroid cancer (TC), and clear renal cell carcinoma (CCRCC). Results Overall, women had a decreased risk of death (HR = 0.73, CI95: 8%-42%), with improved overall survival (OS) in HNC, leukemia, lung cancer, lymphoma, MEL, multiple myeloma (MM), and non-melanoma skin cancer. Regarding the analysis of actionable mutations, only differences in EGFR alterations were observed (27.7% for men vs. 34.4% for women, p = 0.035). The number of differentially activated immune processes was higher in women with HNC, LC, CC, GC, MEL, PC, and TC and included cellular processes, responses to different stimuli, immune system development, immune response activation, multiorganism processes, and localization of immune cells. Only in CCRCC was a higher activation of immune pathways observed in men. Conclusions The study shows an improved survival rate, increased activation of immune system pathways, and an enrichment of EGFR alterations in female patients of our cohort. Enhancement of the immune response in female cancer patients is a phenomenon that should be further explored to improve the efficacy of immunotherapy.
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Affiliation(s)
- Jhajaira M Araujo
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima, Peru.,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Gina Rosas
- Departamento de Patología, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Carolina Belmar-López
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru.,Departamento de Genómica, Oncogenomics, Lima, Peru
| | - Luis E Raez
- Memorial Cancer Institute/Memorial Health Care System, Florida International University (FIU), Pembroke Pines, FL, United States
| | - Christian D Rolfo
- Center for Thoracic Oncology/Tisch Cancer Institute, Mount Sinai, New York, NY, United States
| | - Luis J Schwarz
- Escuela Profesional de Medicina Humana-Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
| | | | - Kevin J Paez
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Luis R García
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Hober Alvarado
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Fany P Ramos
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | | | - Jhon B Cardenas-Farfan
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Melanie Cornejo
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima, Peru
| | | | | | | | - Joseph A Pinto
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima, Peru
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25
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Distinct mechanisms of long-term virologic control in two HIV-infected individuals after treatment interruption of anti-retroviral therapy. Nat Med 2021; 27:1893-1898. [PMID: 34711975 DOI: 10.1038/s41591-021-01503-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/13/2021] [Indexed: 01/02/2023]
Abstract
Certain infected individuals suppress human immunodeficiency virus (HIV) in the absence of anti-retroviral therapy (ART). Elucidating the underlying mechanism(s) is of high interest. Here we present two contrasting case reports of HIV-infected individuals who controlled plasma viremia for extended periods after undergoing analytical treatment interruption (ATI). In Participant 04, who experienced viral blips and initiated undisclosed self-administration of suboptimal ART detected shortly before day 1,250, phylogenetic analyses of plasma HIV env sequences suggested continuous viral evolution and/or reactivation of pre-existing viral reservoirs over time. Antiviral CD8+ T cell activities were higher in Participant 04 than in Participant 30. In contrast, Participant 30 exhibited potent plasma-IgG-mediated neutralization activity against autologous virus that became ineffective when he experienced sudden plasma viral rebound 1,434 d after ATI due to HIV superinfection. Our data provide insight into distinct mechanisms of post-treatment interruption control and highlight the importance of frequent monitoring of undisclosed use of ART and superinfection during the ATI phase.
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26
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Fernandes SJ, Ericsson M, Khademi M, Jagodic M, Olsson T, Gomez-Cabrero D, Kockum I, Tegnér J. Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients. Epigenomics 2021; 13:1607-1618. [PMID: 34676774 DOI: 10.2217/epi-2021-0205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: The putative involvement of chromatin states in multiple sclerosis (MS) is thus far unclear. Here we determined the association of chromatin-accessibility with concurrent genetic, epigenetic and transcriptional events. Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-sequencing profiles from sorted blood immune CD4+ and CD8+ T cells, CD14+ monocytes and CD19+ B cells from healthy controls (HCs) and MS patients. Results: We identified differentially accessible regions between MS patients and HCs, primarily in CD4+ and CD19+. CD4+ regions were enriched for MS-associated single nucleotide polymorphisms and differentially methylated loci. In the vicinity of differentially accessible regions of CD4+ cells, 42 differentially expressed genes were identified. The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1. Conclusion: These findings provide new insight into the primary role of CD4+ and CD19+ cells in MS.
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Affiliation(s)
- Sunjay Jude Fernandes
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, 17165, Sweden.,Science for Life Laboratory, Solna, Stockholm, 17165, Sweden.,Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 17165, Sweden
| | - Matilda Ericsson
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, 17165, Sweden.,Science for Life Laboratory, Solna, Stockholm, 17165, Sweden
| | - Mohsen Khademi
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 17165, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 17165, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 17165, Sweden
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, 17165, Sweden.,Science for Life Laboratory, Solna, Stockholm, 17165, Sweden.,Mucosal & Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK.,Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain.,Biological & Environmental Sciences & Engineering Division, Computer, Electrical & Mathematical Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 17165, Sweden
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, 17165, Sweden.,Science for Life Laboratory, Solna, Stockholm, 17165, Sweden.,Biological & Environmental Sciences & Engineering Division, Computer, Electrical & Mathematical Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
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27
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Zhang Z, Liu L, Shen Y, Meng Z, Chen M, Lu Z, Zhang X. Characterization of chromatin accessibility in psoriasis. Front Med 2021; 16:483-495. [PMID: 34669155 DOI: 10.1007/s11684-021-0872-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/29/2021] [Indexed: 12/13/2022]
Abstract
The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.
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Affiliation(s)
- Zheng Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Lu Liu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Yanyun Shen
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ziyuan Meng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China
| | - Min Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China.,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China
| | - Zhong Lu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Xuejun Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, 200040, China. .,Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, 230032, China. .,Department of Dermatology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215123, China.
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28
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X-linked histone H3K27 demethylase Kdm6a regulates sexually dimorphic differentiation of hypothalamic neurons. Cell Mol Life Sci 2021; 78:7043-7060. [PMID: 34633482 PMCID: PMC8558156 DOI: 10.1007/s00018-021-03945-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022]
Abstract
Several X-linked genes are involved in neuronal differentiation and may contribute to the generation of sex dimorphisms in the brain. Previous results showed that XX hypothalamic neurons grow faster, have longer axons, and exhibit higher expression of the neuritogenic gene neurogenin 3 (Ngn3) than XY before perinatal masculinization. Here we evaluated the participation of candidate X-linked genes in the development of these sex differences, focusing mainly on Kdm6a, a gene encoding for an H3K27 demethylase with functions controlling gene expression genome-wide. We established hypothalamic neuronal cultures from wild-type or transgenic Four Core Genotypes mice, a model that allows evaluating the effect of sex chromosomes independently of gonadal type. X-linked genes Kdm6a, Eif2s3x and Ddx3x showed higher expression in XX compared to XY neurons, regardless of gonadal sex. Moreover, Kdm6a expression pattern with higher mRNA levels in XX than XY did not change with age at E14, P0, and P60 in hypothalamus or under 17β-estradiol treatment in culture. Kdm6a pharmacological blockade by GSK-J4 reduced axonal length only in female neurons and decreased the expression of neuritogenic genes Neurod1, Neurod2 and Cdk5r1 in both sexes equally, while a sex-specific effect was observed in Ngn3. Finally, Kdm6a downregulation using siRNA reduced axonal length and Ngn3 expression only in female neurons, abolishing the sex differences observed in control conditions. Altogether, these results point to Kdm6a as a key mediator of the higher axogenesis and Ngn3 expression observed in XX neurons before the critical period of brain masculinization.
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29
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Fang H, Deng X, Disteche CM. X-factors in human disease: Impact of gene content and dosage regulation. Hum Mol Genet 2021; 30:R285-R295. [PMID: 34387327 DOI: 10.1093/hmg/ddab221] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
The gene content of the X and Y chromosomes has dramatically diverged during evolution. The ensuing dosage imbalance within the genome of males and females has led to unique chromosome-wide regulatory mechanisms with significant and sex-specific impacts on X-linked gene expression. X inactivation or silencing of most genes on one X chromosome chosen at random in females profoundly affects the manifestation of X-linked diseases, as males inherit a single maternal allele, while females express maternal and paternal alleles in a mosaic manner. An additional complication is the existence of genes that escape X inactivation and thus are ubiquitously expressed from both alleles in females. The mosaic nature of X-linked gene expression and the potential for escape can vary between individuals, tissues, cell types, and stages of life. Our understanding of the specialized nature of X-linked genes and of the multilayer epigenetic regulation that influence their expression throughout the organism has been helped by molecular studies conducted by tissue-specific and single-cell-specific approaches. In turn, the definition of molecular events that control X silencing has helped develop new approaches for the treatment of some X-linked disorders. This review focuses on the peculiarities of the X chromosome genetic content and epigenetic regulation in shaping the manifestation of congenital and acquired X-linked disorders in a sex-specific manner.
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Affiliation(s)
- He Fang
- Department of Laboratory Medicine and Pathology
| | | | - Christine M Disteche
- Department of Laboratory Medicine and Pathology.,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
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30
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Éliás S, Schmidt A, Gomez-Cabrero D, Tegnér J. Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells. J Immunol Res 2021; 2021:8880585. [PMID: 34285924 PMCID: PMC8275380 DOI: 10.1155/2021/8880585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 03/14/2021] [Accepted: 03/20/2021] [Indexed: 12/13/2022] Open
Abstract
GM-CSF produced by autoreactive CD4-positive T helper cells is involved in the pathogenesis of autoimmune diseases, such as multiple sclerosis. However, the molecular regulators that establish and maintain the features of GM-CSF-positive CD4 T cells are unknown. In order to identify these regulators, we isolated human GM-CSF-producing CD4 T cells from human peripheral blood by using a cytokine capture assay. We compared these cells to the corresponding GM-CSF-negative fraction, and furthermore, we studied naïve CD4 T cells, memory CD4 T cells, and bulk CD4 T cells from the same individuals as additional control cell populations. As a result, we provide a rich resource of integrated chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) data from these primary human CD4 T cell subsets and we show that the identified signatures are associated with human autoimmune diseases, especially multiple sclerosis. By combining information about mRNA expression, DNA accessibility, and predicted transcription factor binding, we reconstructed directed gene regulatory networks connecting transcription factors to their targets, which comprise putative key regulators of human GM-CSF-positive CD4 T cells as well as memory CD4 T cells. Our results suggest potential therapeutic targets to be investigated in the future in human autoimmune disease.
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Affiliation(s)
- Szabolcs Éliás
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
| | - Angelika Schmidt
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
- Mucosal & Salivary Biology Division, King's College London Dental Institute, London SE1 9RT, UK
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Saudi Arabia
| | - Jesper Tegnér
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, ki.se Karolinska University Hospital & Science for Life Laboratory, 17176 Solna, Stockholm, Sweden
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Saudi Arabia
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31
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Balaton BP, Brown CJ. Contribution of genetic and epigenetic changes to escape from X-chromosome inactivation. Epigenetics Chromatin 2021; 14:30. [PMID: 34187555 PMCID: PMC8244145 DOI: 10.1186/s13072-021-00404-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/17/2021] [Indexed: 01/26/2023] Open
Abstract
Background X-chromosome inactivation (XCI) is the epigenetic inactivation of one of two X chromosomes in XX eutherian mammals. The inactive X chromosome is the result of multiple silencing pathways that act in concert to deposit chromatin changes, including DNA methylation and histone modifications. Yet over 15% of genes escape or variably escape from inactivation and continue to be expressed from the otherwise inactive X chromosome. To the extent that they have been studied, epigenetic marks correlate with this expression. Results Using publicly available data, we compared XCI status calls with DNA methylation, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3. At genes subject to XCI we found heterochromatic marks enriched, and euchromatic marks depleted on the inactive X when compared to the active X. Genes escaping XCI were more similar between the active and inactive X. Using sample-specific XCI status calls, we found some marks differed significantly with variable XCI status, but which marks were significant was not consistent between genes. A model trained to predict XCI status from these epigenetic marks obtained over 75% accuracy for genes escaping and over 90% for genes subject to XCI. This model made novel XCI status calls for genes without allelic differences or CpG islands required for other methods. Examining these calls across a domain of variably escaping genes, we saw XCI status vary across individual genes rather than at the domain level. Lastly, we compared XCI status calls to genetic polymorphisms, finding multiple loci associated with XCI status changes at variably escaping genes, but none individually sufficient to induce an XCI status change. Conclusion The control of expression from the inactive X chromosome is multifaceted, but ultimately regulated at the individual gene level with detectable but limited impact of distant polymorphisms. On the inactive X, at silenced genes euchromatic marks are depleted while heterochromatic marks are enriched. Genes escaping inactivation show a less significant enrichment of heterochromatic marks and depletion of H3K27ac. Combining all examined marks improved XCI status prediction, particularly for genes without CpG islands or polymorphisms, as no single feature is a consistent feature of silenced or expressed genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00404-9.
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Affiliation(s)
- Bradley P Balaton
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.
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32
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Ascierto PA, Bifulco C, Ciardiello F, Demaria S, Emens LA, Ferris R, Formenti SC, Galon J, Khleif SN, Kirchhoff T, McQuade J, Odunsi K, Patnaik A, Paulos CM, Taube JM, Timmerman J, Fox BA, Hwu P, Puzanov I. Perspectives in immunotherapy: meeting report from the immunotherapy bridge (December 2nd-3rd, 2020, Italy). J Transl Med 2021; 19:238. [PMID: 34078406 PMCID: PMC8173810 DOI: 10.1186/s12967-021-02895-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 01/12/2023] Open
Abstract
Improved understanding of tumor immunology has enabled the development of therapies that harness the immune system and prevent immune escape. Numerous clinical trials and real-world experience has provided evidence of the potential for long-term survival with immunotherapy in various types of malignancy. Recurring observations with immuno-oncology agents include their potential for clinical application across a broad patient population with different tumor types, conventional and unconventional response patterns, durable responses, and immune-related adverse events. Despite the substantial achievements to date, a significant proportion of patients still fail to benefit from current immunotherapy options, and ongoing research is focused on transforming non-responders to responders through the development of novel treatments, new strategies to combination therapy, adjuvant and neoadjuvant approaches, and the identification of biomarkers of response. These topics were the focus of the virtual Immunotherapy Bridge (December 2nd-3rd, 2020), organized by the Fondazione Melanoma Onlus, Naples, Italy, in collaboration with the Society for Immunotherapy of Cancer and are summarised in this report.
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Affiliation(s)
- Paolo A Ascierto
- Department of Melanoma, Cancer Immunotherapy and Innovative Therapy, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - Carlo Bifulco
- Providence Cancer Center, Earle A. Chiles Research Institute, Portland, OR, USA
| | - Fortunato Ciardiello
- Medical Oncology and Hematology Division, University "Luigi Vanvitelli", Naples, Italy
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Leisha A Emens
- Magee Women's Hospital, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | | | | | - Jerome Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Paris, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, Paris, France
| | - Samir N Khleif
- The Loop Immuno Oncology Laboratory, Georgetown University Medical School, Washington, DC, USA
| | | | - Jennifer McQuade
- Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA
| | - Akash Patnaik
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | | | - Janis M Taube
- Department of Dermatology, Johns Hopkins University SOM, Baltimore, MD, USA
| | - John Timmerman
- David Geffen School of Medicine, UCLA Medical Center, Los Angeles, CA, USA
| | - Bernard A Fox
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Research Center, Providence Cancer Institute, Portland, OR, USA
| | | | - Igor Puzanov
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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33
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Delshad M, Tavakolinia N, Pourbagheri-Sigaroodi A, Safaroghli-Azar A, Bagheri N, Bashash D. The contributory role of lymphocyte subsets, pathophysiology of lymphopenia and its implication as prognostic and therapeutic opportunity in COVID-19. Int Immunopharmacol 2021; 95:107586. [PMID: 33765611 PMCID: PMC7969831 DOI: 10.1016/j.intimp.2021.107586] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023]
Abstract
The incidence of the novel coronavirus disease (COVID-19) outbreak caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought daunting complications for people as well as physicians around the world. An ever-increasing number of studies investigating the characteristics of the disease, day by day, is shedding light on a new feature of the virus with the hope that eventually these efforts lead to the proper treatment. SARS-CoV-2 activates antiviral immune responses, but in addition may overproduce pro-inflammatory cytokines, causing uncontrolled inflammatory responses in patients with severe COVID-19. This condition may lead to lymphopenia and lymphocyte dysfunction, which in turn, predispose patients to further infections, septic shock, and severe multiple organ dysfunction. Therefore, accurate knowledge in this issue is important to guide clinical management of the disease and the development of new therapeutic strategies in patients with COVID-19. In this review, we provide a piece of valuable information about the alteration of each subtype of lymphocytes and important prognostic factors associated with these cells. Moreover, through discussing the lymphopenia pathophysiology and debating some of the most recent lymphocyte- or lymphopenia-related treatment strategies in COVID-19 patients, we tried to brightening the foreseeable future for COVID-19 patients, especially those with severe disease.
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Affiliation(s)
- Mahda Delshad
- Department of Laboratory Sciences, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Naeimeh Tavakolinia
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ava Safaroghli-Azar
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nader Bagheri
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Corresponding author at: Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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34
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Bakker OB, Ramírez-Sánchez AD, Borek ZA, de Klein N, Li Y, Modderman R, Kooy-Winkelaar Y, Johannesen MK, Matarese F, Martens JHA, Kumar V, van Bergen J, Qiao SW, Lundin KEA, Sollid LM, Koning F, Wijmenga C, Withoff S, Jonkers IH. Potential impact of celiac disease genetic risk factors on T cell receptor signaling in gluten-specific CD4+ T cells. Sci Rep 2021; 11:9252. [PMID: 33927210 PMCID: PMC8085175 DOI: 10.1038/s41598-021-86612-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/18/2021] [Indexed: 02/08/2023] Open
Abstract
Celiac disease is an auto-immune disease in which an immune response to dietary gluten leads to inflammation and subsequent atrophy of small intestinal villi, causing severe bowel discomfort and malabsorption of nutrients. The major instigating factor for the immune response in celiac disease is the activation of gluten-specific CD4+ T cells expressing T cell receptors that recognize gluten peptides presented in the context of HLA-DQ2 and DQ8. Here we provide an in-depth characterization of 28 gluten-specific T cell clones. We assess their transcriptional and epigenetic response to T cell receptor stimulation and link this to genetic factors associated with celiac disease. Gluten-specific T cells have a distinct transcriptional profile that mostly resembles that of Th1 cells but also express cytokines characteristic of other types of T-helper cells. This transcriptional response appears not to be regulated by changes in chromatin state, but rather by early upregulation of transcription factors and non-coding RNAs that likely orchestrate the subsequent activation of genes that play a role in immune pathways. Finally, integration of chromatin and transcription factor binding profiles suggest that genes activated by T cell receptor stimulation of gluten‑specific T cells may be impacted by genetic variation at several genetic loci associated with celiac disease.
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Affiliation(s)
- Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zuzanna A Borek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rutger Modderman
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yvonne Kooy-Winkelaar
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie K Johannesen
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Filomena Matarese
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, 575018, India
| | - Jeroen van Bergen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Shuo-Wang Qiao
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Iris H Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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35
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Balaton BP, Fornes O, Wasserman WW, Brown CJ. Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing. Epigenetics Chromatin 2021; 14:12. [PMID: 33597016 PMCID: PMC7890635 DOI: 10.1186/s13072-021-00386-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Background X-chromosome inactivation (XCI) in eutherian mammals is the epigenetic inactivation of one of the two X chromosomes in XX females in order to compensate for dosage differences with XY males. Not all genes are inactivated, and the proportion escaping from inactivation varies between human and mouse (the two species that have been extensively studied). Results We used DNA methylation to predict the XCI status of X-linked genes with CpG islands across 12 different species: human, chimp, bonobo, gorilla, orangutan, mouse, cow, sheep, goat, pig, horse and dog. We determined the XCI status of 342 CpG islands on average per species, with most species having 80–90% of genes subject to XCI. Mouse was an outlier, with a higher proportion of genes subject to XCI than found in other species. Sixteen genes were found to have discordant X-chromosome inactivation statuses across multiple species, with five of these showing primate-specific escape from XCI. These discordant genes tended to cluster together within the X chromosome, along with genes with similar patterns of escape from XCI. CTCF-binding, ATAC-seq signal and LTR repeats were enriched at genes escaping XCI when compared to genes subject to XCI; however, enrichment was only observed in three or four of the species tested. LINE and DNA repeats showed enrichment around subject genes, but again not in a consistent subset of species. Conclusions In this study, we determined XCI status across 12 species, showing mouse to be an outlier with few genes that escape inactivation. Inactivation status is largely conserved across species. The clustering of genes that change XCI status across species implicates a domain-level control. In contrast, the relatively consistent, but not universal correlation of inactivation status with enrichment of repetitive elements or CTCF binding at promoters demonstrates gene-based influences on inactivation state. This study broadens enrichment analysis of regulatory elements to species beyond human and mouse.
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Affiliation(s)
- Bradley P Balaton
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada
| | - Oriol Fornes
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada
| | - Wyeth W Wasserman
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.
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36
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Morales L, Simpson D, Ferguson R, Cadley J, Esteva E, Monson K, Chat V, Martinez C, Weber J, Osman I, Kirchhoff T. Tumor immunogenomic signatures improve a prognostic model of melanoma survival. J Transl Med 2021; 19:78. [PMID: 33596955 PMCID: PMC7888085 DOI: 10.1186/s12967-021-02738-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/04/2021] [Indexed: 11/10/2022] Open
Abstract
Background Tumor mutation burden (TMB) has been associated with melanoma immunotherapy (IT) outcomes, including survival. We explored whether combining TMB with immunogenomic signatures recently identified by The Cancer Genome Atlas (TCGA) can refine melanoma prognostic models of overall survival (OS) in patients not treated by IT. Methods Cox proportional-hazards (Cox PH) analysis was performed on 278 metastatic melanomas from TCGA not treated by IT. In a discovery and two validation cohorts Cox PH models assessed the interaction between TMB and 53 melanoma immunogenomic features to refine prediction of melanoma OS. Results Interferon-γ response (IFNγRes) and macrophage regulation gene signatures (MacReg) combined with TMB significantly associated with OS (p = 8.80E−14). We observed that patients with high TMB, high IFNγRes and high MacReg had significantly better OS compared to high TMB, low IFNγRes and low MacReg (HR = 2.8, p = 3.55E−08). This association was not observed in low TMB patients. Conclusions We report a model combining TMB and tumor immune features that significantly improves prediction of melanoma OS, independent of IT. Our analysis revealed that patients with high TMB, high levels of IFNγRes and MacReg had significantly more favorable OS compared to high TMB patients with low IFNγRes and low MacReg. These findings may substantially improve current melanoma prognostic models.
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Affiliation(s)
- Leah Morales
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - Danny Simpson
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - Robert Ferguson
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - John Cadley
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - Eduardo Esteva
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - Kelsey Monson
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - Vylyny Chat
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - Carlos Martinez
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA
| | - Jeffrey Weber
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA.,Department of Medicine, NYU Langone Health, New York, USA
| | - Iman Osman
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA.,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA.,Department of Medicine, NYU Langone Health, New York, USA.,Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, USA
| | - Tomas Kirchhoff
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, 522 First Avenue, New York City, NY, 10016, USA. .,Departments of Population Health and Environmental Medicine, NYU Langone Health, New York, USA. .,The Interdisciplinary Melanoma Cooperative Group, NYU Langone Health, New York, USA.
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37
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Wang F, Bai X, Wang Y, Jiang Y, Ai B, Zhang Y, Liu Y, Xu M, Wang Q, Han X, Pan Q, Li Y, Li X, Zhang J, Zhao J, Zhang G, Feng C, Zhu J, Li C. ATACdb: a comprehensive human chromatin accessibility database. Nucleic Acids Res 2021; 49:D55-D64. [PMID: 33125076 PMCID: PMC7779059 DOI: 10.1093/nar/gkaa943] [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] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/05/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022] Open
Abstract
Accessible chromatin is a highly informative structural feature for identifying regulatory elements, which provides a large amount of information about transcriptional activity and gene regulatory mechanisms. Human ATAC-seq datasets are accumulating rapidly, prompting an urgent need to comprehensively collect and effectively process these data. We developed a comprehensive human chromatin accessibility database (ATACdb, http://www.licpathway.net/ATACdb), with the aim of providing a large amount of publicly available resources on human chromatin accessibility data, and to annotate and illustrate potential roles in a tissue/cell type-specific manner. The current version of ATACdb documented a total of 52 078 883 regions from over 1400 ATAC-seq samples. These samples have been manually curated from over 2200 chromatin accessibility samples from NCBI GEO/SRA. To make these datasets more accessible to the research community, ATACdb provides a quality assurance process including four quality control (QC) metrics. ATACdb provides detailed (epi)genetic annotations in chromatin accessibility regions, including super-enhancers, typical enhancers, transcription factors (TFs), common single-nucleotide polymorphisms (SNPs), risk SNPs, eQTLs, LD SNPs, methylations, chromatin interactions and TADs. Especially, ATACdb provides accurate inference of TF footprints within chromatin accessibility regions. ATACdb is a powerful platform that provides the most comprehensive accessible chromatin data, QC, TF footprint and various other annotations.
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Affiliation(s)
- Fan Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yong Zhang
- School of Physics and Electronic Engineering, Northeast Petroleum University, Daqing 163318, China
| | - Yuejuan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Mingcong Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xiaole Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yanyu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jun Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Guorui Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
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38
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Ascierto PA, Butterfield LH, Campbell K, Daniele B, Dougan M, Emens LA, Formenti S, Janku F, Khleif SN, Kirchhoff T, Morabito A, Najjar Y, Nathan P, Odunsi K, Patnaik A, Paulos CM, Reinfeld BI, Skinner HD, Timmerman J, Puzanov I. Perspectives in immunotherapy: meeting report from the "Immunotherapy Bridge" (December 4th-5th, 2019, Naples, Italy). J Transl Med 2021; 19:13. [PMID: 33407605 PMCID: PMC7789268 DOI: 10.1186/s12967-020-02627-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/20/2020] [Indexed: 12/30/2022] Open
Abstract
Over the last few years, numerous clinical trials and real-world experience have provided a large amount of evidence demonstrating the potential for long-term survival with immunotherapy agents across various malignancies, beginning with melanoma and extending to other tumours. The clinical success of immune checkpoint blockade has encouraged increasing development of other immunotherapies. It has been estimated that there are over 3000 immuno-oncology trials ongoing, targeting hundreds of disease and immune pathways. Evolving topics on cancer immunotherapy, including the state of the art of immunotherapy across various malignancies, were the focus of discussions at the Immunotherapy Bridge meeting (4-5 December, 2019, Naples, Italy), and are summarised in this report.
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Affiliation(s)
- Paolo A Ascierto
- Cancer Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Cancer Immunotherapy and Innovative Therapy, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Via Mariano Semmola, 80131, Naples, Italy.
| | - Lisa H Butterfield
- PICI Research & Development, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Katie Campbell
- PICI Research & Development, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | - Michael Dougan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leisha A Emens
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Silvia Formenti
- Sandra and Edward Meyer Cancer Center, Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Filip Janku
- Division of Cancer Medicine, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samir N Khleif
- The Loop Immuno-Oncology Research Laboratory, Lombardi Cancer Center, Georgetown University, Washington, DC, USA
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Alessandro Morabito
- Thoracic Medical Oncology, National Cancer Institute, IRCCS-Fondazione G. Pascale, Naples, Italy
| | - Yana Najjar
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Kunle Odunsi
- Center for Immunotherapy and Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Akash Patnaik
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | | | - Heath D Skinner
- Department of Radiation Oncology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Timmerman
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Igor Puzanov
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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39
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Li K, Wu Y, Li Y, Yu Q, Tian Z, Wei H, Qu K. Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:501-515. [PMID: 33385611 PMCID: PMC8377244 DOI: 10.1016/j.gpb.2020.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/10/2018] [Accepted: 03/04/2019] [Indexed: 12/24/2022]
Abstract
Natural killer (NK) cells are essential in controlling cancer and infection. However, little is known about the dynamics of the transcriptional regulatory machinery during NK cell differentiation. In this study, we applied the assay of transposase accessible chromatin with sequencing (ATAC-seq) technique in a home-developed in vitro NK cell differentiation system. Analysis of ATAC-seq data illustrated two distinct transcription factor (TF) clusters that dynamically regulate NK cell differentiation. Moreover, two TFs from the second cluster, FOS-like 2 (FOSL2) and early growth response 2 (EGR2), were identified as novel essential TFs that control NK cell maturation and function. Knocking down either of these two TFs significantly impacted NK cell differentiation. Finally, we constructed a genome-wide transcriptional regulatory network that provides a better understanding of the regulatory dynamics during NK cell differentiation.
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Affiliation(s)
- Kun Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Yang Wu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Young Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Qiaoni Yu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Zhigang Tian
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China; CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei 230027, China
| | - Haiming Wei
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China; CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei 230027, China.
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China; CAS Center for Excellence in Molecular Cell Sciences, The CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei 230027, China; School of Data Science, University of Science and Technology of China, Hefei 230026, China.
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40
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Peckham H, de Gruijter NM, Raine C, Radziszewska A, Ciurtin C, Wedderburn LR, Rosser EC, Webb K, Deakin CT. Male sex identified by global COVID-19 meta-analysis as a risk factor for death and ITU admission. Nat Commun 2020. [PMID: 33298944 DOI: 10.1038/s41467-020-19741-6.pmid:33298944;pmcid:pmc7726563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Anecdotal evidence suggests that Coronavirus disease 2019 (COVID-19), caused by the coronavirus SARS-CoV-2, exhibits differences in morbidity and mortality between sexes. Here, we present a meta-analysis of 3,111,714 reported global cases to demonstrate that, whilst there is no difference in the proportion of males and females with confirmed COVID-19, male patients have almost three times the odds of requiring intensive treatment unit (ITU) admission (OR = 2.84; 95% CI = 2.06, 3.92) and higher odds of death (OR = 1.39; 95% CI = 1.31, 1.47) compared to females. With few exceptions, the sex bias observed in COVID-19 is a worldwide phenomenon. An appreciation of how sex is influencing COVID-19 outcomes will have important implications for clinical management and mitigation strategies for this disease.
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Affiliation(s)
- Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Nina M de Gruijter
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Charles Raine
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Kate Webb
- Department of Paediatric Rheumatology, School of Child and Adolescent Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa.
- The Francis Crick Institute, Crick African Network, London, UK.
| | - Claire T Deakin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK.
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41
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Peckham H, de Gruijter NM, Raine C, Radziszewska A, Ciurtin C, Wedderburn LR, Rosser EC, Webb K, Deakin CT. Male sex identified by global COVID-19 meta-analysis as a risk factor for death and ITU admission. Nat Commun 2020. [PMID: 33298944 DOI: 10.1038/s41467‐020‐19741‐6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Anecdotal evidence suggests that Coronavirus disease 2019 (COVID-19), caused by the coronavirus SARS-CoV-2, exhibits differences in morbidity and mortality between sexes. Here, we present a meta-analysis of 3,111,714 reported global cases to demonstrate that, whilst there is no difference in the proportion of males and females with confirmed COVID-19, male patients have almost three times the odds of requiring intensive treatment unit (ITU) admission (OR = 2.84; 95% CI = 2.06, 3.92) and higher odds of death (OR = 1.39; 95% CI = 1.31, 1.47) compared to females. With few exceptions, the sex bias observed in COVID-19 is a worldwide phenomenon. An appreciation of how sex is influencing COVID-19 outcomes will have important implications for clinical management and mitigation strategies for this disease.
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Affiliation(s)
- Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.,Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Nina M de Gruijter
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.,Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Charles Raine
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.,Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.,Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.,Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.,Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Kate Webb
- Department of Paediatric Rheumatology, School of Child and Adolescent Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa. .,The Francis Crick Institute, Crick African Network, London, UK.
| | - Claire T Deakin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK. .,Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK. .,NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK.
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42
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Peckham H, de Gruijter NM, Raine C, Radziszewska A, Ciurtin C, Wedderburn LR, Rosser EC, Webb K, Deakin CT. Male sex identified by global COVID-19 meta-analysis as a risk factor for death and ITU admission. Nat Commun 2020; 11:6317. [PMID: 33298944 PMCID: PMC7726563 DOI: 10.1038/s41467-020-19741-6] [Citation(s) in RCA: 833] [Impact Index Per Article: 208.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/23/2020] [Indexed: 12/15/2022] Open
Abstract
Anecdotal evidence suggests that Coronavirus disease 2019 (COVID-19), caused by the coronavirus SARS-CoV-2, exhibits differences in morbidity and mortality between sexes. Here, we present a meta-analysis of 3,111,714 reported global cases to demonstrate that, whilst there is no difference in the proportion of males and females with confirmed COVID-19, male patients have almost three times the odds of requiring intensive treatment unit (ITU) admission (OR = 2.84; 95% CI = 2.06, 3.92) and higher odds of death (OR = 1.39; 95% CI = 1.31, 1.47) compared to females. With few exceptions, the sex bias observed in COVID-19 is a worldwide phenomenon. An appreciation of how sex is influencing COVID-19 outcomes will have important implications for clinical management and mitigation strategies for this disease.
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Affiliation(s)
- Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Nina M de Gruijter
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Charles Raine
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Anna Radziszewska
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK
- Centre for Rheumatology Research, Division of Medicine, UCL, London, UK
| | - Kate Webb
- Department of Paediatric Rheumatology, School of Child and Adolescent Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa.
- The Francis Crick Institute, Crick African Network, London, UK.
| | - Claire T Deakin
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH, GOSH, London, UK.
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK.
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Liu Q, Zaba LC, Satpathy AT, Longmire M, Zhang W, Li K, Granja J, Guo C, Lin J, Li R, Tolentino K, Kania G, Distler O, Fiorentino D, Chung L, Qu K, Chang HY. Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis. Nat Commun 2020; 11:5843. [PMID: 33203843 PMCID: PMC7672105 DOI: 10.1038/s41467-020-19702-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022] Open
Abstract
Systemic sclerosis (SSc) is a disease at the intersection of autoimmunity and fibrosis. However, the epigenetic regulation and the contributions of diverse cell types to SSc remain unclear. Here we survey, using ATAC-seq, the active DNA regulatory elements of eight types of primary cells in normal skin from healthy controls, as well as clinically affected and unaffected skin from SSc patients. We find that accessible DNA elements in skin-resident dendritic cells (DCs) exhibit the highest enrichment of SSc-associated single-nucleotide polymorphisms (SNPs) and predict the degrees of skin fibrosis in patients. DCs also have the greatest disease-associated changes in chromatin accessibility and the strongest alteration of cell-cell interactions in SSc lesions. Lastly, data from an independent cohort of patients with SSc confirm a significant increase of DCs in lesioned skin. Thus, the DCs epigenome links inherited susceptibility and clinically apparent fibrosis in SSc skin, and can be an important driver of SSc pathogenesis.
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Affiliation(s)
- Qian Liu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Lisa C Zaba
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Longmire
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Wen Zhang
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Kun Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jeffrey Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chuang Guo
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Jun Lin
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gabriela Kania
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - David Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lorinda Chung
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
- CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230027, China.
- School of Data Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Linher-Melville K, Shah A, Singh G. Sex differences in neuro(auto)immunity and chronic sciatic nerve pain. Biol Sex Differ 2020; 11:62. [PMID: 33183347 PMCID: PMC7661171 DOI: 10.1186/s13293-020-00339-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/20/2020] [Indexed: 01/13/2023] Open
Abstract
Chronic pain occurs with greater frequency in women, with a parallel sexually dimorphic trend reported in sufferers of many autoimmune diseases. There is a need to continue examining neuro-immune-endocrine crosstalk in the context of sexual dimorphisms in chronic pain. Several phenomena in particular need to be further explored. In patients, autoantibodies to neural antigens have been associated with sensory pathway hyper-excitability, and the role of self-antigens released by damaged nerves remains to be defined. In addition, specific immune cells release pro-nociceptive cytokines that directly influence neural firing, while T lymphocytes activated by specific antigens secrete factors that either support nerve repair or exacerbate the damage. Modulating specific immune cell populations could therefore be a means to promote nerve recovery, with sex-specific outcomes. Understanding biological sex differences that maintain, or fail to maintain, neuroimmune homeostasis may inform the selection of sex-specific treatment regimens, improving chronic pain management by rebalancing neuroimmune feedback. Given the significance of interactions between nerves and immune cells in the generation and maintenance of neuropathic pain, this review focuses on sex differences and possible links with persistent autoimmune activity using sciatica as an example.
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Affiliation(s)
- Katja Linher-Melville
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Pain Research and Care, McMaster University, Hamilton, Ontario, Canada
| | - Anita Shah
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Gurmit Singh
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.
- Michael G. DeGroote Institute for Pain Research and Care, McMaster University, Hamilton, Ontario, Canada.
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45
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Hauberg ME, Creus-Muncunill J, Bendl J, Kozlenkov A, Zeng B, Corwin C, Chowdhury S, Kranz H, Hurd YL, Wegner M, Børglum AD, Dracheva S, Ehrlich ME, Fullard JF, Roussos P. Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons. Nat Commun 2020; 11:5581. [PMID: 33149216 PMCID: PMC7643171 DOI: 10.1038/s41467-020-19319-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/08/2020] [Indexed: 01/04/2023] Open
Abstract
The chromatin landscape of human brain cells encompasses key information to understanding brain function. Here we use ATAC-seq to profile the chromatin structure in four distinct populations of cells (glutamatergic neurons, GABAergic neurons, oligodendrocytes, and microglia/astrocytes) from three different brain regions (anterior cingulate cortex, dorsolateral prefrontal cortex, and primary visual cortex) in human postmortem brain samples. We find that chromatin accessibility varies greatly by cell type and, more moderately, by brain region, with glutamatergic neurons showing the largest regional variability. Transcription factor footprinting implicates cell-specific transcriptional regulators and infers cell-specific regulation of protein-coding genes, long intergenic noncoding RNAs and microRNAs. In vivo transgenic mouse experiments validate the cell type specificity of several of these human-derived regulatory sequences. We find that open chromatin regions in glutamatergic neurons are enriched for neuropsychiatric risk variants, particularly those associated with schizophrenia. Integration of cell-specific chromatin data with a bulk tissue study of schizophrenia brains increases statistical power and confirms that glutamatergic neurons are most affected. These findings illustrate the utility of studying the cell-type-specific epigenome in complex tissues like the human brain, and the potential of such approaches to better understand the genetic basis of human brain function.
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Affiliation(s)
- Mads E Hauberg
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Jordi Creus-Muncunill
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaroslav Bendl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Biao Zeng
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chuhyon Corwin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Chowdhury
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harald Kranz
- Gene Bridges, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
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46
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Zhao Y, Zhang X, Song Z, Wei D, Wang H, Chen W, Sun G, Ma W, Chen K. Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection. Front Med (Lausanne) 2020; 7:584728. [PMID: 33224964 PMCID: PMC7670091 DOI: 10.3389/fmed.2020.584728] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is associated with significant progress in biological research and has attracted increasing attention. However, the impact of ATAC-seq on cancer biology has not been objectively analyzed. We categorized 440 ATAC-seq publications according to the publication date, type, field, and country. R 3.6.2 was used to analyze the distribution of research fields. VOSviewer was used for country co-authorship and author co-authorship analyses, and GraphPad Prism 8 was used for correlation analyses of the factors that may affect the number of articles published in different countries. We found that ATAC-seq plays roles in carcinogenesis, anticancer immunity, targeted therapy, and metastasis risk predictions and is most frequently used in studies of leukemia among all types of cancer. We found a significantly strong correlation between the top 10 countries in terms of the number of publications and the gross expenditure on research and development (R&D), the number of universities, and the number of researchers. At present, ATAC-seq technology is undergoing a period of rapid development, making it inseparable from the emphasis and investment in scientific research by many countries. Collectively, ATAC-seq has advantages in the study of the cancer mechanisms because it can detect nucleic acids and thus has good application prospects in the field of cancer, especially in leukemia studies. As a country's economic strength increases and the emphasis on scientific research deepens, ATAC-seq will definitely play a more significant role in the field of cancer biology.
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Affiliation(s)
- Yu Zhao
- Department of Hematology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Xianwen Zhang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenhua Song
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Treatment Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
| | - Danian Wei
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Treatment Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
| | - Hong Wang
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,Academy of Orthopedics of Guangdong Province, Guangzhou, China
| | - Wei Chen
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Musculoskeletal Oncology, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
| | - Guodong Sun
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weiying Ma
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Kebing Chen
- Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Disease, Department of Spine Surgery, The Third Affiliated Hospital of Southern Medical University (Academy of Orthopedics of Guangdong Province), Guangzhou, China
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47
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Vavalà T, Rigney M, Reale ML, Novello S, King JC. An examination of two dichotomies: Women with lung cancer and living with lung cancer as a chronic disease. Respirology 2020; 25 Suppl 2:24-36. [PMID: 33124087 DOI: 10.1111/resp.13965] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/14/2022]
Abstract
Lung cancer remains the leading cause of cancer death globally, yet with many recent advances in the diagnosis and treatment of lung cancer, the face of the disease is shifting. Historically, lung cancer is often thought of as a predominantly male disease with more than twice as many men as women being diagnosed worldwide-mostly due to the influence of smoking as the leading risk factor. However, lung cancer is also the second leading cause of cancer death in women and there is a growing population of young women who have never smoked and are being diagnosed. The past decade has seen groundbreaking innovations in both the early detection and treatment of lung cancer. In this new era, survival rates are beginning to increase and many of those diagnosed are finding themselves in a new situation-living long term with a deadly cancer. Here, we review pertinent aspects of women and lung cancer as well as the concept of living with lung cancer as a chronic disease to give a new perspective on the changing face of lung cancer treatment and care.
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Affiliation(s)
| | | | - Maria Lucia Reale
- Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
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48
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A Unique Epigenomic Landscape Defines Human Erythropoiesis. Cell Rep 2020; 28:2996-3009.e7. [PMID: 31509757 PMCID: PMC6863094 DOI: 10.1016/j.celrep.2019.08.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/28/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022] Open
Abstract
Mammalian erythropoiesis yields a highly specialized cell type, the mature erythrocyte, evolved to meet the organismal needs of increased oxygen-carrying capacity. To better understand the regulation of erythropoiesis, we performed genome-wide studies of chromatin accessibility, DNA methylation, and transcriptomics using a recently developed strategy to obtain highly purified populations of primary human erythroid cells. The integration of gene expression, DNA methylation, and chromatin state dynamics reveals that stage-specific gene regulation during erythropoiesis is a stepwise and hierarchical process involving many cis-regulatory elements. Erythroid-specific, nonpromoter sites of chromatin accessibility are linked to erythroid cell phenotypic variation and inherited disease. Comparative analyses of stage-specific chromatin accessibility indicate that there is limited early chromatin priming of erythroid genes during hematopoiesis. The epigenome of terminally differentiating erythroid cells defines a distinct subset of highly specialized cells that are vastly dissimilar from other hematopoietic and nonhematopoietic cell types. These epigenomic and transcriptome data are powerful tools to study human erythropoiesis. Schulz et al. use genome-wide studies of chromatin accessibility, DNA methylation, and transcriptomes in primary human erythroid cells to reveal important characteristics of erythropoiesis. Chromatin accessibility of terminal erythroid differentiation is markedly dissimilar from other hematopoietic cell types. Epigenomic changes are linked to erythroid cell traits and disease genes.
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49
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Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis. Cell Rep 2020; 27:3228-3240.e7. [PMID: 31189107 PMCID: PMC6579117 DOI: 10.1016/j.celrep.2019.05.046] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/03/2019] [Accepted: 05/14/2019] [Indexed: 02/01/2023] Open
Abstract
Human erythropoiesis serves as a paradigm of physiologic cellular differentiation. This process is also of considerable interest for better understanding anemias and identifying new therapies. Here, we apply deep transcriptomic and accessible chromatin profiling to characterize a faithful ex vivo human erythroid differentiation system from hematopoietic stem and progenitor cells. We reveal stage-specific transcriptional states and chromatin accessibility during various stages of erythropoiesis, including 14,260 differentially expressed genes and 63,659 variably accessible chromatin peaks. Our analysis suggests differentiation stage-predominant roles for specific master regulators, including GATA1 and KLF1. We integrate chromatin profiles with common and rare genetic variants associated with erythroid cell traits and diseases, finding that variants regulating different erythroid phenotypes likely act at variable points during differentiation. In addition, we identify a regulator of terminal erythropoiesis, TMCC2, more broadly illustrating the value of this comprehensive analysis to improve our understanding of erythropoiesis in health and disease. Ludwig et al. chart the dynamic transcriptional and chromatin landscapes as hematopoietic stem and progenitor cells differentiate into mature red blood cells. This multi-omic profiling reveals dynamic transcription factor activities and human genetic variation that modulate this process.
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50
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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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