1
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Kim KM, D'Elia AM, Rodell CB. Hydrogel-based approaches to target hypersensitivity mechanisms underlying autoimmune disease. Adv Drug Deliv Rev 2024; 212:115395. [PMID: 39004347 DOI: 10.1016/j.addr.2024.115395] [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: 11/08/2023] [Revised: 06/23/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
A robust adaptive immune response is essential for combatting pathogens. In the wrong context such as due to genetic and environmental factors, however, the same mechanisms crucial for self-preservation can lead to a loss of self-tolerance. Resulting autoimmunity manifests in the development of a host of organ-specific or systemic autoimmune diseases, hallmarked by aberrant immune responses and tissue damage. The prevalence of autoimmune diseases is on the rise, medical management of which focuses primarily on pharmacological immunosuppression that places patients at a risk of side effects, including opportunistic infections and tumorigenesis. Biomaterial-based drug delivery systems confer many opportunities to address challenges associated with conventional disease management. Hydrogels, in particular, can protect encapsulated cargo (drug or cell therapeutics) from the host environment, afford their presentation in a controlled manner, and can be tailored to respond to disease conditions or support treatment via multiplexed functionality. Moreover, localized delivery to affected sites by these approaches has the potential to concentrate drug action at the site, reduce off-target exposure, and enhance patient compliance by reducing the need for frequent administration. Despite their many benefits for the management of autoimmune disease, such biomaterial-based approaches focus largely on the downstream effects of hypersensitivity mechanisms and have a limited capacity to eradicate the disease. In contrast, direct targeting of mechanisms of hypersensitivity reactions uniquely enables prophylaxis or the arrest of disease progression by mitigating the basis of autoimmunity. One promising approach is to induce self-antigen-specific tolerance, which specifically subdues damaging autoreactivity while otherwise retaining the normal immune responses. In this review, we will discuss hydrogel-based systems for the treatment of autoimmune disease, with a focus on those that target hypersensitivity mechanisms head-on. As the field continues to advance, it will expand the range of therapeutic choices for people coping with autoimmune diseases, providing fresh prospects for better clinical outcomes and improved quality of life.
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Affiliation(s)
- Kenneth M Kim
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
| | - Arielle M D'Elia
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA.
| | - Christopher B Rodell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA; School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA.
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2
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Qi T, Song L, Guo Y, Chen C, Yang J. From genetic associations to genes: methods, applications, and challenges. Trends Genet 2024; 40:642-667. [PMID: 38734482 DOI: 10.1016/j.tig.2024.04.008] [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: 11/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Genome-wide association studies (GWASs) have identified numerous genetic loci associated with human traits and diseases. However, pinpointing the causal genes remains a challenge, which impedes the translation of GWAS findings into biological insights and medical applications. In this review, we provide an in-depth overview of the methods and technologies used for prioritizing genes from GWAS loci, including gene-based association tests, integrative analysis of GWAS and molecular quantitative trait loci (xQTL) data, linking GWAS variants to target genes through enhancer-gene connection maps, and network-based prioritization. We also outline strategies for generating context-dependent xQTL data and their applications in gene prioritization. We further highlight the potential of gene prioritization in drug repurposing. Lastly, we discuss future challenges and opportunities in this field.
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Affiliation(s)
- Ting Qi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
| | - Liyang Song
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yazhou Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Chang Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Jian Yang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
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3
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Garavito-De Egea G, Domínguez-Vargas A, Vélez JI, Aroca G, Fang L, Navarro-Quiroz E, Espitaleta Z, Del Toro-Camargo K, Martínez-Ariza L, González-Vargas T, García S, Arcos-Burgos M, Egea E. Common interacting genetic variation shapes susceptibility to type 1 diabetes in a Colombian Caribbean community: In search of shared genetic markers. Genes Dis 2024; 11:101058. [PMID: 38510475 PMCID: PMC10951448 DOI: 10.1016/j.gendis.2023.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/27/2023] [Indexed: 03/22/2024] Open
Affiliation(s)
- Gloria Garavito-De Egea
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
| | | | - Jorge I. Vélez
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
| | - Gustavo Aroca
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
- Clínica de la Costa, Grupo de Investigación en Nefrología, Barranquilla, Colombia
| | - Luis Fang
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
| | - Elkin Navarro-Quiroz
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
| | - Zilac Espitaleta
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
- Clínica de la Costa, Grupo de Investigación en Nefrología, Barranquilla, Colombia
| | | | | | | | - Susana García
- Clínica de la Costa, Grupo de Investigación en Nefrología, Barranquilla, Colombia
| | - Mauricio Arcos-Burgos
- Universidad de Antioquia, Grupo de Investigación en Psiquiatría (GIPSI), Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Medellín, Colombia
| | - Eduardo Egea
- Universidad del Norte, División Ciencias de la Salud, Barranquilla, Colombia
- Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
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4
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Ramírez-Valle F, Maranville JC, Roy S, Plenge RM. Sequential immunotherapy: towards cures for autoimmunity. Nat Rev Drug Discov 2024; 23:501-524. [PMID: 38839912 DOI: 10.1038/s41573-024-00959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Abstract
Despite major progress in the treatment of autoimmune diseases in the past two decades, most therapies do not cure disease and can be associated with increased risk of infection through broad suppression of the immune system. However, advances in understanding the causes of autoimmune disease and clinical data from novel therapeutic modalities such as chimeric antigen receptor T cell therapies provide evidence that it may be possible to re-establish immune homeostasis and, potentially, prolong remission or even cure autoimmune diseases. Here, we propose a 'sequential immunotherapy' framework for immune system modulation to help achieve this ambitious goal. This framework encompasses three steps: controlling inflammation; resetting the immune system through elimination of pathogenic immune memory cells; and promoting and maintaining immune homeostasis via immune regulatory agents and tissue repair. We discuss existing drugs and those in development for each of the three steps. We also highlight the importance of causal human biology in identifying and prioritizing novel immunotherapeutic strategies as well as informing their application in specific patient subsets, enabling precision medicine approaches that have the potential to transform clinical care.
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5
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Zou Y, Carbonetto P, Xie D, Wang G, Stephens M. Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.14.536893. [PMID: 37425935 PMCID: PMC10327118 DOI: 10.1101/2023.04.14.536893] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
We introduce mvSuSiE, a multi-trait fine-mapping method for identifying putative causal variants from genetic association data (individual-level or summary data). mvSuSiE learns patterns of shared genetic effects from data, and exploits these patterns to improve power to identify causal SNPs. Comparisons on simulated data show that mvSuSiE is competitive in speed, power and precision with existing multi-trait methods, and uniformly improves on single-trait fine-mapping (SuSiE) in each trait separately. We applied mvSuSiE to jointly fine-map 16 blood cell traits using data from the UK Biobank. By jointly analyzing the traits and modeling heterogeneous effect sharing patterns, we discovered a much larger number of causal SNPs (>3,000) compared with single-trait fine-mapping, and with narrower credible sets. mvSuSiE also more comprehensively characterized the ways in which the genetic variants affect one or more blood cell traits; 68% of causal SNPs showed significant effects in more than one blood cell type.
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Affiliation(s)
- Yuxin Zou
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Dongyue Xie
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Gao Wang
- Gertrude. H. Sergievsky Center, Department of Neurology, Columbia University, New York, NY, USA
| | - Matthew Stephens
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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6
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Trefilio LM, Bottino L, de Carvalho Cardoso R, Montes GC, Fontes-Dantas FL. The impact of genetic variants related to vitamin D and autoimmunity: A systematic review. Heliyon 2024; 10:e27700. [PMID: 38689997 PMCID: PMC11059421 DOI: 10.1016/j.heliyon.2024.e27700] [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: 09/19/2023] [Revised: 02/14/2024] [Accepted: 03/05/2024] [Indexed: 05/02/2024] Open
Abstract
Over the past few years, there has been a notable increment in scientific literature aimed at unraveling the genetic foundations of vitamin D signaling and its implications for susceptibility to autoimmunity, however, most of them address isolated diseases. Here, we conducted a systematic review of genetic variants related to vitamin D and autoimmune diseases and we discussed the current landscape of susceptibility and outcomes. Of 65 studies analyzed, most variants cited are in vitamin D binding protein (VDBP; rs2282679 GC gene), 25-hydroxylase (rs10751657 CYP2R1), 1α-hydroxylase (rs10877012, CYP27B1) and the nuclear hormone receptor superfamily [FokI (rs2228570), BsmI (rs1544410), ApaI (rs7975232), and TaqI (rs731236) in VDR gene]. Therefore, our findings confirmed the associations of several genetic variants of vitamin D signaling with a broad spectrum of autoimmune diseases/traits. In addition, given the low number of papers found with functional analysis, further studies to elucidate the real effect that the variants exert on Vitamin D signaling are recommended.
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Affiliation(s)
- Luisa Menezes Trefilio
- Universidade Estadual do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Farmacologia e Psicobiologia, Rio de Janeiro RJ, Brazil
- Universidade Federal do Estado do Rio de Janeiro, Instituto Biomédico, Rio de Janeiro RJ, Brazil
| | - Letícia Bottino
- Universidade Estadual do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Farmacologia e Psicobiologia, Rio de Janeiro RJ, Brazil
- Universidade Federal do Estado do Rio de Janeiro, Escola de Medicina, Rio de Janeiro RJ, Brazil
| | - Rafaella de Carvalho Cardoso
- Universidade Estadual do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Farmacologia e Psicobiologia, Rio de Janeiro RJ, Brazil
- Universidade Estadual do Rio de Janeiro, Programa de Pós-Graduação em Fisiopatologia Clínica e Experimental, Rio de Janeiro RJ, Brazil
| | - Guilherme Carneiro Montes
- Universidade Estadual do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Farmacologia e Psicobiologia, Rio de Janeiro RJ, Brazil
- Universidade Estadual do Rio de Janeiro, Programa de Pós-Graduação em Fisiopatologia Clínica e Experimental, Rio de Janeiro RJ, Brazil
| | - Fabrícia Lima Fontes-Dantas
- Universidade Estadual do Rio de Janeiro, Instituto de Biologia Roberto Alcântara Gomes, Departamento de Farmacologia e Psicobiologia, Rio de Janeiro RJ, Brazil
- Universidade Estadual do Rio de Janeiro, Programa de Pós-Graduação em Fisiopatologia Clínica e Experimental, Rio de Janeiro RJ, Brazil
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7
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Tian R, Ghosh S. Mechanisms and functions of lncRNAs linked to autoimmune disease risk alleles. Adv Immunol 2024; 161:1-15. [PMID: 38763698 DOI: 10.1016/bs.ai.2024.03.006] [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: 05/21/2024]
Abstract
Recent advances in human genomics technologies have helped uncover genetic risk alleles for many complex autoimmune diseases. Intriguingly, over 90% of genome-wide association study (GWAS) risk alleles reside within the non-coding regions of the genome. An emerging new frontier of functional and mechanistic studies have shed light on the functional relevance of risk alleles that lie within long noncoding RNAs (lncRNAs). Here, we review the mechanisms and functional implications of five evolutionarily conserved lncRNAs that display risk allele association with highly prevalent autoimmune diseases.
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Affiliation(s)
- Ruxiao Tian
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States
| | - Sankar Ghosh
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States.
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8
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Mohammed J, Arora N, Matthews HS, Hansen K, Bader M, Walsh S, Shaffer JR, Weinberg SM, Swigut T, Claes P, Selleri L, Wysocka J. A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis. eLife 2024; 13:e82564. [PMID: 38483448 PMCID: PMC10939500 DOI: 10.7554/elife.82564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/18/2024] [Indexed: 03/17/2024] Open
Abstract
Genome-wide association studies (GWAS) identified thousands of genetic variants linked to phenotypic traits and disease risk. However, mechanistic understanding of how GWAS variants influence complex morphological traits and can, in certain cases, simultaneously confer normal-range phenotypic variation and disease predisposition, is still largely lacking. Here, we focus on rs6740960, a single nucleotide polymorphism (SNP) at the 2p21 locus, which in GWAS studies has been associated both with normal-range variation in jaw shape and with an increased risk of non-syndromic orofacial clefting. Using in vitro derived embryonic cell types relevant for human facial morphogenesis, we show that this SNP resides in an enhancer that regulates chondrocytic expression of PKDCC - a gene encoding a tyrosine kinase involved in chondrogenesis and skeletal development. In agreement, we demonstrate that the rs6740960 SNP is sufficient to confer chondrocyte-specific differences in PKDCC expression. By deploying dense landmark morphometric analysis of skull elements in mice, we show that changes in Pkdcc dosage are associated with quantitative changes in the maxilla, mandible, and palatine bone shape that are concordant with the facial phenotypes and disease predisposition seen in humans. We further demonstrate that the frequency of the rs6740960 variant strongly deviated among different human populations, and that the activity of its cognate enhancer diverged in hominids. Our study provides a mechanistic explanation of how a common SNP can mediate normal-range and disease-associated morphological variation, with implications for the evolution of human facial features.
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Affiliation(s)
- Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Harold S Matthews
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Susan Walsh
- Department of Biology, Indiana University IndianapolisIndianapolisUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
- Department of Anthropology, University of PittsburghPittsburghUnited States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Peter Claes
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
- Department of Electrical Engineering, ESAT/PSI, KU LeuvenLeuvenBelgium
- Murdoch Children’s Research InstituteMelbourneAustralia
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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9
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Li H, Yu Z, Du F, Song L, Gao Y, Shi F. sscNOVA: a semi-supervised convolutional neural network for predicting functional regulatory variants in autoimmune diseases. Front Immunol 2024; 15:1323072. [PMID: 38380333 PMCID: PMC10876991 DOI: 10.3389/fimmu.2024.1323072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/15/2024] [Indexed: 02/22/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified thousands of variants in the human genome with autoimmune diseases. However, identifying functional regulatory variants associated with autoimmune diseases remains challenging, largely because of insufficient experimental validation data. We adopt the concept of semi-supervised learning by combining labeled and unlabeled data to develop a deep learning-based algorithm framework, sscNOVA, to predict functional regulatory variants in autoimmune diseases and analyze the functional characteristics of these regulatory variants. Compared to traditional supervised learning methods, our approach leverages more variants' data to explore the relationship between functional regulatory variants and autoimmune diseases. Based on the experimentally curated testing dataset and evaluation metrics, we find that sscNOVA outperforms other state-of-the-art methods. Furthermore, we illustrate that sscNOVA can help to improve the prioritization of functional regulatory variants from lead single-nucleotide polymorphisms and the proxy variants in autoimmune GWAS data.
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Affiliation(s)
- Haibo Li
- School of Information Engineering, Ningxia University, Yinchuan, China
| | - Zhenhua Yu
- School of Information Engineering, Ningxia University, Yinchuan, China
- Collaborative Innovation Center for Ningxia Big Data and Artificial Intelligence Co-founded by Ningxia Municipality and Ministry of Education, Yinchuan, Ningxia University, Yinchuan, China
| | - Fang Du
- School of Information Engineering, Ningxia University, Yinchuan, China
- Collaborative Innovation Center for Ningxia Big Data and Artificial Intelligence Co-founded by Ningxia Municipality and Ministry of Education, Yinchuan, Ningxia University, Yinchuan, China
| | - Lijuan Song
- School of Information Engineering, Ningxia University, Yinchuan, China
- Collaborative Innovation Center for Ningxia Big Data and Artificial Intelligence Co-founded by Ningxia Municipality and Ministry of Education, Yinchuan, Ningxia University, Yinchuan, China
| | - Yang Gao
- School of Medical Technology, North Minzu University, Yinchuan, China
| | - Fangyuan Shi
- School of Information Engineering, Ningxia University, Yinchuan, China
- Collaborative Innovation Center for Ningxia Big Data and Artificial Intelligence Co-founded by Ningxia Municipality and Ministry of Education, Yinchuan, Ningxia University, Yinchuan, China
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10
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Jin H, Arase H. Neoself Antigens Presented on MHC Class II Molecules in Autoimmune Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:51-65. [PMID: 38467972 DOI: 10.1007/978-981-99-9781-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Major histocompatibility complex (MHC) class II molecules play a crucial role in immunity by presenting peptide antigens to helper T cells. Immune cells are generally tolerant to self-antigens. However, when self-tolerance is broken, immune cells attack normal tissues or cells, leading to the development of autoimmune diseases. Genome-wide association studies have shown that MHC class II is the gene most strongly associated with the risk of most autoimmune diseases. When misfolded self-antigens, called neoself antigens, are associated with MHC class II molecules in the endoplasmic reticulum, they are transported by the MHC class II molecules to the cell surface without being processed into peptides. Moreover, neoself antigens that are complexed with MHC class II molecules of autoimmune disease risk alleles exhibit distinct antigenicities compared to normal self-antigens, making them the primary targets of autoantibodies in various autoimmune diseases. Elucidation of the immunological functions of neoself antigens presented on MHC class II molecules is crucial for understanding the mechanism of autoimmune diseases.
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Affiliation(s)
- Hui Jin
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
- Laboratory of Immunochemistry, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan.
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan.
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11
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Lv JH, Hou AJ, Zhang SH, Dong JJ, Kuang HX, Yang L, Jiang H. WGCNA combined with machine learning to find potential biomarkers of liver cancer. Medicine (Baltimore) 2023; 102:e36536. [PMID: 38115320 PMCID: PMC10727608 DOI: 10.1097/md.0000000000036536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023] Open
Abstract
The incidence of hepatocellular carcinoma (HCC) has been increasing in recent years. With the development of various detection technologies, machine learning is an effective method to screen disease characteristic genes. In this study, weighted gene co-expression network analysis (WGCNA) and machine learning are combined to find potential biomarkers of liver cancer, which provides a new idea for future prediction, prevention, and personalized treatment. In this study, the "limma" software package was used. P < .05 and log2 |fold-change| > 1 is the standard screening differential genes, and then the module genes obtained by WGCNA analysis are crossed to obtain the key module genes. Gene Ontology and Kyoto Gene and Genome Encyclopedia analysis was performed on key module genes, and 3 machine learning methods including lasso, support vector machine-recursive feature elimination, and RandomForest were used to screen feature genes. Finally, the validation set was used to verify the feature genes, the GeneMANIA (http://www.genemania.org) database was used to perform protein-protein interaction networks analysis on the feature genes, and the SPIED3 database was used to find potential small molecule drugs. In this study, 187 genes associated with HCC were screened by using the "limma" software package and WGCNA. After that, 6 feature genes (AADAT, APOF, GPC3, LPA, MASP1, and NAT2) were selected by RandomForest, Absolute Shrinkage and Selection Operator, and support vector machine-recursive feature elimination machine learning algorithms. These genes are also significantly different on the external dataset and follow the same trend as the training set. Finally, our findings may provide new insights into targets for diagnosis, prevention, and treatment of HCC. AADAT, APOF, GPC3, LPA, MASP1, and NAT2 may be potential genes for the prediction, prevention, and treatment of liver cancer in the future.
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Affiliation(s)
- Jia-Hao Lv
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - A-Jiao Hou
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Shi-Hao Zhang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Jiao-Jiao Dong
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Hai-Xue Kuang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Liu Yang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
| | - Hai Jiang
- Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, China
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12
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Wang Z, Liu T, Li W, Yu G, Mi Z, Wang C, Liao X, Huai P, Chu T, Liu D, Sun L, Fu X, Sun Y, Wang H, Wang N, Liu J, Liu H, Zhang F. Genome-wide meta-analysis and fine-mapping prioritize potential causal variants and genes related to leprosy. MedComm (Beijing) 2023; 4:e415. [PMID: 38020709 PMCID: PMC10674079 DOI: 10.1002/mco2.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/05/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
To date, genome-wide association studies (GWASs) have discovered 35 susceptible loci of leprosy; however, the cumulative effects of these loci can only partially explain the overall risk of leprosy, and the causal variants and genes within these loci remain unknown. Here, we conducted out new GWASs in two independent cohorts of 5007 cases and 4579 controls and then a meta-analysis in these newly generated and multiple previously published (2277 cases and 3159 controls) datasets were performed. Three novel and 15 previously reported risk loci were identified from these datasets, increasing the known leprosy risk loci of explained genetic heritability from 23.0 to 38.5%. A comprehensive fine-mapping analysis was conducted, and 19 causal variants and 14 causal genes were identified. Specifically, manual checking of epigenomic information from the Epimap database revealed that the causal variants were mainly located within the immune-relevant or immune-specific regulatory elements. Furthermore, by using gene-set, tissue, and cell-type enrichment analyses, we highlighted the key roles of immune-related tissues and cells and implicated the PD-1 signaling pathways in the pathogenetic mechanism of leprosy. Collectively, our study identified candidate causal variants and elucidated the potential regulatory and coding mechanisms for genes associated with leprosy.
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Affiliation(s)
- Zhenzhen Wang
- Department of BiostatisticsSchool of Public HealthCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Tingting Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Wenchao Li
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Gongqi Yu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Zihao Mi
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Chuan Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Xiaojie Liao
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Pengcheng Huai
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Tongsheng Chu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Dianchang Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Lele Sun
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Xi'an Fu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Yonghu Sun
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Honglei Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Na Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Jianjun Liu
- Department of Human Genetics, Genome Institute of SingaporeSingaporeSingapore
| | - Hong Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Furen Zhang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
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13
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Innate and adaptive immune abnormalities underlying autoimmune diseases: the genetic connections. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-021-2187-3. [PMID: 36738430 PMCID: PMC9898710 DOI: 10.1007/s11427-021-2187-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/10/2022] [Indexed: 02/05/2023]
Abstract
With the exception of an extremely small number of cases caused by single gene mutations, most autoimmune diseases result from the complex interplay between environmental and genetic factors. In a nutshell, etiology of the common autoimmune disorders is unknown in spite of progress elucidating certain effector cells and molecules responsible for pathologies associated with inflammatory and tissue damage. In recent years, population genetics approaches have greatly enriched our knowledge regarding genetic susceptibility of autoimmunity, providing us with a window of opportunities to comprehensively re-examine autoimmunity-associated genes and possible pathways. In this review, we aim to discuss etiology and pathogenesis of common autoimmune disorders from the perspective of human genetics. An overview of the genetic basis of autoimmunity is followed by 3 chapters detailing susceptibility genes involved in innate immunity, adaptive immunity and inflammatory cell death processes respectively. With such attempts, we hope to expand the scope of thinking and bring attention to lesser appreciated molecules and pathways as important contributors of autoimmunity beyond the 'usual suspects' of a limited subset of validated therapeutic targets.
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14
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Kridin K, Lyakhovitsky K, Tzur-Bitan D, Onn E, Lyakhovitsky A, Zoller L, Cohen AD. Vitiligo and systemic sclerosis: Are they associated?- Lessons from a population-based study. Australas J Dermatol 2023; 64:e65-e71. [PMID: 36326157 DOI: 10.1111/ajd.13942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/26/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The epidemiological relationship of vitiligo with systemic sclerosis (SSc) remains to be precisely evaluated. OBJECTIVE To investigate the bidirectional association between vitiligo and SSc. METHODS A population-based study was carried out to compare vitiligo patients (n = 20,851) with age-, sex- and ethnicity-matched control subjects (n = 102,475) regarding the incidence of new-onset and the prevalence of preexisting SSc. Adjusted hazard ratios (HRs) and adjusted odds ratios (ORs) were calculated by the Cox regression and logistic regression, respectively. RESULTS The incidence rate of new-onset SSc was calculated at 2.4 (95% CI, 1.6-3.4) and 0.4 (95% CI, 0.3-0.6) cases per 10,000 person-years among patients with vitiligo and controls, respectively. Patients with vitiligo had an increased risk of SSc (fully adjusted HR, 5.37; 95% CI, 3.03-9.54; p < 0.001). Correspondingly, a history of SSc predicted elevated odds of developing vitiligo (fully adjusted OR, 2.09; 95% CI, 1.23-3.55; p = 0.006). Relative to other patients with vitiligo, those with vitiligo and comorbid SSc were older and had a higher prevalence of ischaemic heart disease, hyperlipidaemia, and hypertension. CONCLUSIONS A robust bidirectional association exists between vitiligo and SSc. This knowledge is valuable for physicians managing patients with both conditions. Patients with vitiligo and comorbid SSc might be monitored for cardiovascular and metabolic comorbidities.
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Affiliation(s)
- Khalaf Kridin
- Unit of Dermatology and Skin Research Laboratory, Baruch Padeh Medical Center, Poriya, Israel.,Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | - Dana Tzur-Bitan
- Department of Behavioral Sciences, Ariel University, Ariel, Israel.,Shalvata Mental Health Center, Hod Hasharon, affiliated with the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Erez Onn
- Baruch Padeh Medical Center, Poriya, Israel
| | - Anna Lyakhovitsky
- Department of Dermatology, Sheba Medical Center, Tel-Hashomer, Ramat-Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lilach Zoller
- Clalit Health Services, Tel-Aviv and Haifa, Tel Aviv, Israel
| | - Arnon D Cohen
- Clalit Health Services, Tel-Aviv and Haifa, Tel Aviv, Israel.,Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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15
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Miller FW. The increasing prevalence of autoimmunity and autoimmune diseases: an urgent call to action for improved understanding, diagnosis, treatment, and prevention. Curr Opin Immunol 2023; 80:102266. [PMID: 36446151 PMCID: PMC9918670 DOI: 10.1016/j.coi.2022.102266] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/04/2022] [Indexed: 11/27/2022]
Abstract
Autoimmunity is characterized by self-reactive immune components and autoimmune disease by autoimmunity plus pathology. Both autoimmunity and autoimmune diseases are dramatically increasing in many parts of the world, likely as a result of changes in our exposures to environmental factors. Current evidence implicates the momentous alterations in our foods, xenobiotics, air pollution, infections, personal lifestyles, stress, and climate change as causes for these increases. Autoimmune diseases have a major impact on the individuals and families they affect, as well as on our society and healthcare costs, and current projections suggest they may soon take their place among the predominant medical disorders. This necessitates that we increase the scope and scale of our efforts, and coordinate our resources and studies, to understand autoimmune disease risk factors and pathogeneses and improve our diagnostic, therapeutic, and preventive approaches, as the costs of inaction will be profound and far greater without such investments.
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Affiliation(s)
- Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bldg. 101, Maildrop A2-03, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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16
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Implications of Post-Translational Modifications in Autoimmunity with Emphasis on Citrullination, Homocitrullination and Acetylation for the Pathogenesis, Diagnosis and Prognosis of Rheumatoid Arthritis. Int J Mol Sci 2022; 23:ijms232415803. [PMID: 36555449 PMCID: PMC9781636 DOI: 10.3390/ijms232415803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTMs) influence cellular processes and consequently, their dysregulation is related to the etiologies of numerous diseases. It is widely known that a variety of autoimmune responses in human diseases depend on PTMs of self-proteins. In this review we summarize the latest findings about the role of PTMs in the generation of autoimmunity and, specifically, we address the most relevant PTMs in rheumatic diseases that occur in synovial tissue. Citrullination, homocitrullination (carbamylation) and acetylation are responsible for the generation of Anti-Modified Protein/Peptide Antibodies (AMPAs family), autoantibodies which have been implicated in the etiopathogenesis, diagnosis and prognosis of rheumatoid arthritis (RA). Synthetic peptides provide complete control over the exact epitopes presented as well as the specific positions in their sequence where post-translationally modified amino acids are located and are key to advancing the detection of serological RA biomarkers that could be useful to stratify RA patients in order to pursue a personalized rheumatology. In this review we specifically address the latest findings regarding synthetic peptides post-translationally modified for the specific detection of autoantibodies in RA patients.
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17
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Huang M, Xu H. Genetic susceptibility to autoimmunity-Current status and challenges. Adv Immunol 2022; 156:25-54. [PMID: 36410874 DOI: 10.1016/bs.ai.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Autoimmune diseases (ADs) often arise from a combination of genetic and environmental triggers that disrupt the immune system's capability to properly tolerate body self-antigens. Familial studies provided the earliest insights into the risk loci of such diseases, while genome-wide association studies (GWAS) significantly broadened the horizons. A drug targeting a prominent pathological pathway can be applied to multiple indications sharing overlapping mechanisms. Advances in genomic technologies used in genetic studies provide critical insights into future research on gene-environment interactions in autoimmunity. This Review summarizes the history and recent advances in the understanding of genetic susceptibility to ADs and related immune disorders, including coronavirus disease 2019 (COVID-19), and their indications for the development of diagnostic or prognostic markers for translational applications.
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Affiliation(s)
| | - Huji Xu
- School of Medicine, Tsinghua University, Beijing, China; Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Navel Medical University, Shanghai, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China.
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18
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Jacobs BM, Peter M, Giovannoni G, Noyce AJ, Morris HR, Dobson R. Towards a global view of multiple sclerosis genetics. Nat Rev Neurol 2022; 18:613-623. [PMID: 36075979 DOI: 10.1038/s41582-022-00704-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a neuroimmunological disorder of the CNS with a strong heritable component. The genetic architecture of MS susceptibility is well understood in populations of European ancestry. However, the extent to which this architecture explains MS susceptibility in populations of non-European ancestry remains unclear. In this Perspective article, we outline the scientific arguments for studying MS genetics in ancestrally diverse populations. We argue that this approach is likely to yield insights that could benefit individuals with MS from all ancestral groups. We explore the logistical and theoretical challenges that have held back this field to date and conclude that, despite these challenges, inclusion of participants of non-European ancestry in MS genetics studies will ultimately be of value to all patients with MS worldwide.
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Affiliation(s)
- Benjamin Meir Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK. .,Department of Neurology, Royal London Hospital, London, UK.
| | - Michelle Peter
- NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Blizard Institute, Queen Mary University London, London, UK
| | - Alastair J Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Huw R Morris
- Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
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19
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Ashton JJ, Seaby EG, Beattie RM, Ennis S. NOD2 in Crohn's disease- unfinished business. J Crohns Colitis 2022; 17:450-458. [PMID: 36006803 PMCID: PMC10069614 DOI: 10.1093/ecco-jcc/jjac124] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 01/01/2023]
Abstract
Studies of Crohn's disease consistently implicate NOD2 as the most important gene in disease pathogenesis since first being identified in 2001. Since this point, genome-wide association, next-generation sequencing, and functional analyses have all confirmed a key role for NOD2, but despite this, NOD2 also has significant unresolved complexity. More recent studies have reinvigorated an early hypothesis that NOD2 may be a single-gene cause of disease, and the distinct ileal stricturing phenotype seen with NOD2-related disease presents an opportunity for personalised diagnosis, disease prediction and targeted therapy. The genomics of NOD2 has much that remains unknown, including the role of rare variation, phasing of variants across the haplotype block and the role of variation in the NOD2-regulatory regions. Here, we discuss the evidence and the unmet needs of NOD2-research, based on recently published evidence, and suggest methods that may meet these requirements.
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Affiliation(s)
- James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Eleanor G Seaby
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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20
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Li Y, Jiang W, Mellins ED. TCR-like antibodies targeting autoantigen-mhc complexes: a mini-review. Front Immunol 2022; 13:968432. [PMID: 35967436 PMCID: PMC9363607 DOI: 10.3389/fimmu.2022.968432] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
T cell receptors (TCRs) recognize peptide antigens bound to major histocompatibility complex (MHC) molecules (p/MHC) that are expressed on cell surfaces; while B cell-derived antibodies (Abs) recognize soluble or cell surface native antigens of various types (proteins, carbohydrates, etc.). Immune surveillance by T and B cells thus inspects almost all formats of antigens to mount adaptive immune responses against cancer cells, infectious organisms and other foreign insults, while maintaining tolerance to self-tissues. With contributions from environmental triggers, the development of autoimmune disease is thought to be due to the expression of MHC risk alleles by antigen-presenting cells (APCs) presenting self-antigen (autoantigen), breaking through self-tolerance and activating autoreactive T cells, which orchestrate downstream pathologic events. Investigating and treating autoimmune diseases have been challenging, both because of the intrinsic complexity of these diseases and the need for tools targeting T cell epitopes (autoantigen-MHC). Naturally occurring TCRs with relatively low (micromolar) affinities to p/MHC are suboptimal for autoantigen-MHC targeting, whereas the use of engineered TCRs and their derivatives (e.g., TCR multimers and TCR-engineered T cells) are limited by unpredictable cross-reactivity. As Abs generally have nanomolar affinity, recent advances in engineering TCR-like (TCRL) Abs promise advantages over their TCR counterparts for autoantigen-MHC targeting. Here, we compare the p/MHC binding by TCRs and TCRL Abs, review the strategies for generation of TCRL Abs, highlight their application for identification of autoantigen-presenting APCs, and discuss future directions and limitations of TCRL Abs as immunotherapy for autoimmune diseases.
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Affiliation(s)
- Ying Li
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Wei Jiang
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Wei Jiang, ; Elizabeth D. Mellins,
| | - Elizabeth D. Mellins
- Department of Pediatrics, Divisions of Human Gene Therapy and Allergy, Immunology & Rheumatology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Wei Jiang, ; Elizabeth D. Mellins,
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21
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Szukiewicz D. Epigenetic regulation and T-cell responses in endometriosis – something other than autoimmunity. Front Immunol 2022; 13:943839. [PMID: 35935991 PMCID: PMC9355085 DOI: 10.3389/fimmu.2022.943839] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Endometriosis is defined as the presence of endometrial-like glands and stroma located outside the uterine cavity. This common, estrogen dependent, inflammatory condition affects up to 15% of reproductive-aged women and is a well-recognized cause of chronic pelvic pain and infertility. Despite the still unknown etiology of endometriosis, much evidence suggests the participation of epigenetic mechanisms in the disease etiopathogenesis. The main rationale is based on the fact that heritable phenotype changes that do not involve alterations in the DNA sequence are common triggers for hormonal, immunological, and inflammatory disorders, which play a key role in the formation of endometriotic foci. Epigenetic mechanisms regulating T-cell responses, including DNA methylation and posttranslational histone modifications, deserve attention because tissue-resident T lymphocytes work in concert with organ structural cells to generate appropriate immune responses and are functionally shaped by organ-specific environmental conditions. Thus, a failure to precisely regulate immune cell transcription may result in compromised immunological integrity of the organ with an increased risk of inflammatory disorders. The coexistence of endometriosis and autoimmunity is a well-known occurrence. Recent research results indicate regulatory T-cell (Treg) alterations in endometriosis, and an increased number of highly active Tregs and macrophages have been found in peritoneal fluid from women with endometriosis. Elimination of the regulatory function of T cells and an imbalance between T helper cells of the Th1 and Th2 types have been reported in the endometria of women with endometriosis-associated infertility. This review aims to present the state of the art in recognition epigenetic reprogramming of T cells as the key factor in the pathophysiology of endometriosis in the context of T-cell-related autoimmunity. The new potential therapeutic approaches based on epigenetic modulation and/or adoptive transfer of T cells will also be outlined.
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22
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Jadidi N, Alesaeidi S, Arab F, Pakzad B, Siasi E, Esmaeilzadeh E. miRNA-binding site polymorphism in IL-15RA gene in rheumatoid arthritis and systemic lupus erythematosus: correlation with disease risk and clinical characteristics. Clin Rheumatol 2022; 41:3487-3494. [PMID: 35857215 DOI: 10.1007/s10067-022-06298-6] [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: 04/17/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION/OBJECTIVES MiRSNPs may interfere with mRNA stability through effects on microRNAs (miRNAs)-mRNA interactions via direct changes in miRNA binding site or effect on the secondary structure of this region and changes in accessibility of this region to miRNAs. Studies have confirmed that an elevated level of interleukin-15 receptor alpha (IL-15RA) has an important role in the pathogenesis of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). In the present study, for the first time, we aimed to evaluate the possible correlation between a miRSNP, rs2296135, in IL-15RA gene with the risk of SLE and RA. METHODS In this case-control study, 100 SLE patients, 100 RA patients, and 110 healthy participants were enrolled to assess rs2296135 genotypes with real-time PCR high-resolution melting method. RESULTS According to our findings, AA genotype and A allele of rs2296135 were considerably associated with enhanced risk of RA (for AA genotype, OR = 2.29; 95% CI [1.06-5.02]; for A allele, OR = 1.65; 95% CI [1.10-2.48]). However, this common variant was not significantly correlated with SLE risk in population under study. Stratification analysis in the RA group verified that patients with the A allele had considerably higher serum concentrations of C-reactive protein (CRP) (P < 0.001). In SLE subjects, the frequency of arthritis (P: 0.021) and renal involvement (P: 0.025) in patients with A allele was significantly higher than in other SLE individuals. CONCLUSION The current study proposes a substantial association between rs2296135 polymorphism in IL-15RA gene with augmented risk of RA and some clinical characteristics in RA and SLE patients.
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Affiliation(s)
- Nilofar Jadidi
- Department of Genetics, Faculty of Basic Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran.,Department of Biology, Faculty of Basic Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Samira Alesaeidi
- Rheumatology and Internal Medicine, Rheumatology Research Center, Amir-Alam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Arab
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Pakzad
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Elham Siasi
- Department of Genetics, Faculty of Basic Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Emran Esmaeilzadeh
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran. .,Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran.
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23
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Nguyen K, Alsaati N, Le Coz C, Romberg N. Genetic obstacles to developing and tolerizing human B cells. WIREs Mech Dis 2022; 14:e1554. [DOI: 10.1002/wsbm.1554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Kim Nguyen
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Nouf Alsaati
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Carole Le Coz
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | - Neil Romberg
- Division of Immunology and Allergy Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
- Department of Pediatrics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Institute for Immunology University of Pennsylvania Philadelphia Pennsylvania USA
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24
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Christophersen A, Dahal‐Koirala S, Chlubnová M, Jahnsen J, Lundin KEA, Sollid LM. Phenotype-Based Isolation of Antigen-Specific CD4 + T Cells in Autoimmunity: A Study of Celiac Disease. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104766. [PMID: 35119226 PMCID: PMC8981484 DOI: 10.1002/advs.202104766] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/08/2022] [Indexed: 05/15/2023]
Abstract
The pathogenic immune response in celiac disease (CeD) is orchestrated by phenotypically distinct CD4+ T cells that recognize gluten epitopes in the context of disease-associated HLA-DQ allotypes. Cells with the same distinct phenotype, but with elusive specificities, are increased across multiple autoimmune conditions. Here, whether sorting of T cells based on their distinct phenotype (Tphe cells) yields gluten-reactive cells in CeD is tested. The method's efficiency is benchmarked by parallel isolation of gluten-reactive T cells (Ttet cells), using HLA-DQ:gluten peptide tetramers. From gut biopsies of 12 untreated HLA-DQ2.5+ CeD patients, Ttet+ /Tphe+ , Ttet- /Tphe+ , and Ttet- /Tphe- cells are sorted for single-cell T-cell receptor (TCR)-sequencing (n = 8) and T-cell clone (TCC)-generation (n = 5). The generated TCCs are TCR sequenced and tested for their reactivity against deamidated gluten. Gluten-reactivity is observed in 91.2% of Ttet+ /Tphe+ TCCs, 65.3% of Ttet- /Tphe+ TCCs and 0% of Ttet- /Tphe- TCCs. TCR sequencing reveals clonal expansion and sequence sharing across patients, features reflecting antigen-driven responses. The feasibility to isolate antigen-specific CD4+ T cells by the sole use of phenotypic markers in CeD outlines a potential avenue for characterizing disease-driving CD4+ T cells in autoimmune conditions.
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Affiliation(s)
- Asbjørn Christophersen
- KG Jebsen Coeliac Disease Research CentreUniversity of OsloOslo0372Norway
- Institute of Clinical MedicineUniversity of OsloOslo0450Norway
- Department of RheumatologyDermatology and Infectious DiseasesOslo University HospitalOslo0372Norway
| | - Shiva Dahal‐Koirala
- KG Jebsen Coeliac Disease Research CentreUniversity of OsloOslo0372Norway
- Institute of Clinical MedicineUniversity of OsloOslo0450Norway
| | - Markéta Chlubnová
- KG Jebsen Coeliac Disease Research CentreUniversity of OsloOslo0372Norway
- Institute of Clinical MedicineUniversity of OsloOslo0450Norway
| | - Jørgen Jahnsen
- Department of GastroenterologyAkershus University HospitalLørenskog1478Norway
| | - Knut E. A. Lundin
- KG Jebsen Coeliac Disease Research CentreUniversity of OsloOslo0372Norway
- Institute of Clinical MedicineUniversity of OsloOslo0450Norway
- Department of GastroenterologyOslo University Hospital RikshospitaletOslo0372Norway
| | - Ludvig M. Sollid
- KG Jebsen Coeliac Disease Research CentreUniversity of OsloOslo0372Norway
- Institute of Clinical MedicineUniversity of OsloOslo0450Norway
- Department of ImmunologyOslo University HospitalOslo0372Norway
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25
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Zeinalzadeh S, Kheradmand N, Rasouli G, Esmaeilzadeh E, Pakzad B, Behroozi J, Chamanara M, Zoshk MY, Ehtesham N, Sabet MN. Association of a miRNA-binding site polymorphism in IL-16 gene with disease risk and clinical characteristics of rheumatoid arthritis and systemic lupus erythematosus. Clin Rheumatol 2022; 41:2189-2196. [PMID: 35332405 DOI: 10.1007/s10067-022-06131-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/16/2022] [Accepted: 03/13/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION /objectives. Single nucleotide polymorphisms (SNPs) located at the 3'-UTR region of the target genes of microRNAs (miRNAs) can dysregulate their expression via disrupting the binding site of miRNAs. Interleukin-16 (IL-16) is involved in the pathogenesis of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). In the current study, we assessed the possible association between rs1131445 polymorphism in IL-16 gene with risk and clinical characteristics of RA and SLE in the Iranian population. METHODS In this case-control study, 120 patients with RA, 120 patients with SLE, and 120 unrelated healthy subjects were collected to estimate rs1131445 (T > C) polymorphism in IL-16 gene using real-time PCR high-resolution melting (HRM) method. RESULTS Our results demonstrated considerable associations between TC genotype and C allele of rs1131445 with enhanced risk of RA (ORfor TC genotype = 3.01; 95%CI [1.667-5.526], P < 0.001; ORfor C allele = 1.96; 95%CI [1.314-2.941], P < 0.001). Besides, there was a marginal association between CC genotype and increased risk of RA (P: 0.031). However, there was an insignificant correlation between genotypes and allele frequencies of rs1131445 with incidence risk of SLE (P > 0.05). Moreover, stratification analysis indicated that the C allele in rs1131445 was linked with disease activity-associated laboratory parameters such as CRP and ESR in both RA and SLE patients, as well as the higher incidence of neurological symptoms in SLE subjects (P < 0.05). CONCLUSION These results proposed a significant association between IL-16 polymorphism and augmented risk of RA and clinical characteristics of RA and SLE.
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Affiliation(s)
| | - Nahid Kheradmand
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghazal Rasouli
- Faculty of Basic Sciences, Central Tehran Branch, Islamic Azad University, Isfahan, Iran
| | | | - Bahram Pakzad
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Javad Behroozi
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran, Iran.,Department of Genetics and Advanced Medical Technology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohsen Chamanara
- Toxicology Research Center, Aja University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, School of Medicine, Aja University of Medical Sciences, Tehran, Iran
| | | | - Naeim Ehtesham
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
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26
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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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27
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Saurabh R, Fouodo CJK, König IR, Busch H, Wohlers I. A survey of genome-wide association studies, polygenic scores and UK Biobank highlights resources for autoimmune disease genetics. Front Immunol 2022; 13:972107. [PMID: 35990650 PMCID: PMC9388859 DOI: 10.3389/fimmu.2022.972107] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Autoimmune diseases share a general mechanism of auto-antigens harming tissues. Still. they are phenotypically diverse, with genetic as well as environmental factors contributing to their etiology at varying degrees. Associated genomic loci and variants have been identified in numerous genome-wide association studies (GWAS), whose results are increasingly used for polygenic scores (PGS) that are used to predict disease risk. At the same time, a technological shift from genotyping arrays to next generation sequencing (NGS) is ongoing. NGS allows the identification of virtually all - including rare - genetic variants, which in combination with methodological developments promises to improve the prediction of disease risk and elucidate molecular mechanisms underlying disease. Here we review current, publicly available autoimmune disease GWAS and PGS data based on information from the GWAS and PGS catalog, respectively. We summarize autoimmune diseases investigated, respective studies conducted and their results. Further, we review genetic data and autoimmune disease patients in the UK Biobank (UKB), the largest resource for genetic and phenotypic data available for academic research. We find that only comparably prevalent autoimmune diseases are covered by the UKB and at the same time assessed by both GWAS and PGS catalogs. These are systemic (systemic lupus erythematosus) as well as organ-specific, affecting the gastrointestinal tract (inflammatory bowel disease as well as specifically Crohn's disease and ulcerative colitis), joints (juvenile ideopathic arthritis, psoriatic arthritis, rheumatoid arthritis, ankylosing spondylitis), glands (Sjögren syndrome), the nervous system (multiple sclerosis), and the skin (vitiligo).
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Affiliation(s)
- Rochi Saurabh
- Medical Systems Biology, Lübeck Institute for Experimental Dermatology (LIED) and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Césaire J K Fouodo
- Institute of Medical Biometry and Statistics (IMBS), University of Lübeck, Lübeck, Germany
| | - Inke R König
- Institute of Medical Biometry and Statistics (IMBS), University of Lübeck, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology, Lübeck Institute for Experimental Dermatology (LIED) and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Inken Wohlers
- Medical Systems Biology, Lübeck Institute for Experimental Dermatology (LIED) and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
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