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Hafeez R, Guo J, Ahmed T, Jiang H, Raza M, Shahid M, Ibrahim E, Wang Y, Wang J, Yan C, An Q, White JC, Li B. Bio-formulated chitosan nanoparticles enhance disease resistance against rice blast by physiomorphic, transcriptional, and microbiome modulation of rice (Oryza sativa L.). Carbohydr Polym 2024; 334:122023. [PMID: 38553222 DOI: 10.1016/j.carbpol.2024.122023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/02/2024]
Abstract
Rice blast disease (RBD) caused by Magnaporthe oryzae, threaten food security by cutting agricultural output. Nano agrochemicals are now perceived as sustainable, cost-effective alternatives to traditional pesticides. This study investigated bioformulation of moringa chitosan nanoparticles (M-CsNPs) and their mechanisms for suppressing RBD while minimizing toxic effects on the microenvironment. M-CsNPs, sized 46 nm with semi-spherical morphology, significantly suppressed pathogen growth, integrity, and colonization at 200 mg L-1in vitro. Greenhouse tests with foliar exposure to the same concentration resulted in a substantial 77.7 % reduction in RBD, enhancing antioxidant enzyme activity and plant health. Furthermore, M-CsNPs improved photosynthesis, gas exchange, and the nutritional profile of diseased rice plants. RNA-seq analysis highlighted upregulated defense-related genes in treated rice plants. Metagenomic study showcased reshaping of the rice microbiome, reducing Magnaporthe abundance by 93.5 %. Both healthy and diseased rice plants showed increased microbial diversity, particularly favoring specific beneficial species Thiobacillus, Nitrospira, Nocardioides, and Sphingomicrobium in the rhizosphere and Azonexus, Agarivorans, and Bradyrhizobium in the phyllosphere. This comprehensive study unravels the diverse mechanisms by which M-CsNPs interact with plants and pathogens, curbing M. oryzae damage, promoting plant growth, and modulating the rice microbiome. It underscores the significant potential for effective plant disease management.
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Affiliation(s)
- Rahila Hafeez
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Junning Guo
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Xianghu Laboratory, Hangzhou 311231, China; MEU Research Unit, Middle East University, Amman, Jordan
| | - Hubiao Jiang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mubashar Raza
- Key Laboratory of Integrated Pest Management on Crops in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang 830091, China
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Ezzeldin Ibrahim
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yanli Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiaoyu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | - Chengqi Yan
- Crop Institute, Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Qianli An
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT, USA.
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Lincoln MR, Connally N, Axisa PP, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers IH, Padyukov L, Rich SS, Graham RR, Gaffney PM, Langefeld CD, Vyse TJ, Hafler DA, Chun S, Sunyaev SR, Cotsapas C. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nat Genet 2024; 56:10.1038/s41588-024-01732-8. [PMID: 38741015 DOI: 10.1038/s41588-024-01732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/21/2024] [Indexed: 05/16/2024]
Abstract
Autoimmune and inflammatory diseases are polygenic disorders of the immune system. Many genomic loci harbor risk alleles for several diseases, but the limited resolution of genetic mapping prevents determining whether the same allele is responsible, indicating a shared underlying mechanism. Here, using a collection of 129,058 cases and controls across 6 diseases, we show that ~40% of overlapping associations are due to the same allele. We improve fine-mapping resolution for shared alleles twofold by combining cases and controls across diseases, allowing us to identify more expression quantitative trait loci driven by the shared alleles. The patterns indicate widespread sharing of pathogenic mechanisms but not a single global autoimmune mechanism. Our approach can be applied to any set of traits and is particularly valuable as sample collections become depleted.
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Affiliation(s)
- Matthew R Lincoln
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Division of Neurology at the Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Noah Connally
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Pierre-Paul Axisa
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mitja Mitrovic
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - David van Heel
- Blizard Institute, Queen Mary University of London, London, UK
| | - Cisca Wijmenga
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Iris H Jonkers
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Leonid Padyukov
- Division of Rheumatology at the Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Robert R Graham
- Maze Therapeutics, South San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Vesalius Therapeutics, Cambridge, MA, USA.
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Zou Y, Pan M, Zhou T, Yan L, Chen Y, Yun J, Wang Z, Guo H, Zhang K, Xiong W. Critical COVID-19, Victivallaceae abundance, and celiac disease: A mediation Mendelian randomization study. PLoS One 2024; 19:e0301998. [PMID: 38701071 PMCID: PMC11068179 DOI: 10.1371/journal.pone.0301998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/26/2024] [Indexed: 05/05/2024] Open
Abstract
Celiac disease exhibits a higher prevalence among patients with coronavirus disease 2019. However, the potential influence of COVID-19 on celiac disease remains uncertain. Considering the significant association between gut microbiota alterations, COVID-19 and celiac disease, the two-step Mendelian randomization method was employed to investigate the genetic causality between COVID-19 and celiac disease, with gut microbiota as the potential mediators. We employed the genome-wide association study to select genetic instrumental variables associated with the exposure. Subsequently, these variables were utilized to evaluate the impact of COVID-19 on the risk of celiac disease and its potential influence on gut microbiota. Employing a two-step Mendelian randomization approach enabled the examination of potential causal relationships, encompassing: 1) the effects of COVID-19 infection, hospitalized COVID-19 and critical COVID-19 on the risk of celiac disease; 2) the influence of gut microbiota on celiac disease; and 3) the mediating impact of the gut microbiota between COVID-19 and the risk of celiac disease. Our findings revealed a significant association between critical COVID-19 and an elevated risk of celiac disease (inverse variance weighted [IVW]: P = 0.035). Furthermore, we observed an inverse correlation between critical COVID-19 and the abundance of Victivallaceae (IVW: P = 0.045). Notably, an increased Victivallaceae abundance exhibits a protective effect against the risk of celiac disease (IVW: P = 0.016). In conclusion, our analysis provides genetic evidence supporting the causal connection between critical COVID-19 and lower Victivallaceae abundance, thereby increasing the risk of celiac disease.
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Affiliation(s)
- Yuxin Zou
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Manyi Pan
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyu Zhou
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifeng Yan
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuntian Chen
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junjie Yun
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihua Wang
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaqi Guo
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Zhang
- Department of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weining Xiong
- Department of Respiratory and Critical Care Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Wen J, Zhang J, Zhang H, Zhang N, Lei R, Deng Y, Cheng Q, Li H, Luo P. Large-scale genome-wide association studies reveal the genetic causal etiology between air pollutants and autoimmune diseases. J Transl Med 2024; 22:392. [PMID: 38685026 PMCID: PMC11057084 DOI: 10.1186/s12967-024-04928-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/23/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Epidemiological evidence links a close correlation between long-term exposure to air pollutants and autoimmune diseases, while the causality remained unknown. METHODS Two-sample Mendelian randomization (TSMR) was used to investigate the role of PM10, PM2.5, NO2, and NOX (N = 423,796-456,380) in 15 autoimmune diseases (N = 14,890-314,995) using data from large European GWASs including UKB, FINNGEN, IMSGC, and IPSCSG. Multivariable Mendelian randomization (MVMR) was conducted to investigate the direct effect of each air pollutant and the mediating role of common factors, including body mass index (BMI), alcohol consumption, smoking status, and household income. Transcriptome-wide association studies (TWAS), two-step MR, and colocalization analyses were performed to explore underlying mechanisms between air pollution and autoimmune diseases. RESULTS In TSMR, after correction of multiple testing, hypothyroidism was causally associated with higher exposure to NO2 [odds ratio (OR): 1.37, p = 9.08 × 10-4] and NOX [OR: 1.34, p = 2.86 × 10-3], ulcerative colitis (UC) was causally associated with higher exposure to NOX [OR: 2.24, p = 1.23 × 10-2] and PM2.5 [OR: 2.60, p = 5.96 × 10-3], rheumatoid arthritis was causally associated with higher exposure to NOX [OR: 1.72, p = 1.50 × 10-2], systemic lupus erythematosus was causally associated with higher exposure to NOX [OR: 4.92, p = 6.89 × 10-3], celiac disease was causally associated with lower exposure to NOX [OR: 0.14, p = 6.74 × 10-4] and PM2.5 [OR: 0.17, p = 3.18 × 10-3]. The risky effects of PM2.5 on UC remained significant in MVMR analyses after adjusting for other air pollutants. MVMR revealed several common mediators between air pollutants and autoimmune diseases. Transcriptional analysis identified specific gene transcripts and pathways interconnecting air pollutants and autoimmune diseases. Two-step MR revealed that POR, HSPA1B, and BRD2 might mediate from air pollutants to autoimmune diseases. POR pQTL (rs59882870, PPH4=1.00) strongly colocalized with autoimmune diseases. CONCLUSION This research underscores the necessity of rigorous air pollutant surveillance within public health studies to curb the prevalence of autoimmune diseases.
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Affiliation(s)
- Jie Wen
- The Animal Laboratory Center, Hunan Cancer Hospital, and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jingwei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Nan Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ruoyan Lei
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yujia Deng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- First Clinical Department, Changsha Medical University, Changsha, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.
- Hypothalamic Pituitary Research Centre, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - He Li
- The Animal Laboratory Center, Hunan Cancer Hospital, and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Abadie V, Han A, Jabri B, Sollid LM. New Insights on Genes, Gluten, and Immunopathogenesis of Celiac Disease. Gastroenterology 2024:S0016-5085(24)00478-5. [PMID: 38670280 DOI: 10.1053/j.gastro.2024.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024]
Abstract
Celiac disease (CeD) is a gluten-induced enteropathy that develops in genetically susceptible individuals upon consumption of cereal gluten proteins. It is a unique and complex immune disorder to study, as the driving antigen is known and the tissue targeted by the immune reaction can be interrogated. This review integrates findings gained from genetic, biochemical, and immunologic studies, which together have revealed mechanisms of gluten peptide modification and HLA binding, thereby enabling a maladapted anti-gluten immune response. Observations in human samples combined with experimental mouse models have revealed that the gluten-induced immune response involves CD4+ T cells, cytotoxic CD8+ T cells, and B cells; their cross-talks are critical for the tissue-damaging response. The emergence of high-throughput technologies is increasing our understanding of the phenotype, location, and presumably function of the gluten-specific cells, which are all required to identify novel therapeutic targets and strategies for CeD.
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Affiliation(s)
- Valérie Abadie
- Department of Medicine, The University of Chicago, Chicago, Illinois; Section of Gastroenterology, Nutrition and Hepatology, The University of Chicago, Chicago, Illinois; Committee on Immunology, The University of Chicago, Chicago, Illinois.
| | - Arnold Han
- Columbia Center for Translational Immunology, Columbia University, New York, New York; Department of Microbiology and Immunology, Columbia University, New York, New York; Department of Medicine, Digestive and Liver Diseases, Columbia University, New York, New York; Department of Medicine, Digestive and Liver Diseases, Columbia University, New York, New York
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, Illinois; Section of Gastroenterology, Nutrition and Hepatology, The University of Chicago, Chicago, Illinois; Committee on Immunology, The University of Chicago, Chicago, Illinois; Department of Pathology, University of Chicago, Chicago, Illinois; Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Ludvig M Sollid
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
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Perez-Quintero LA, Abidin BM, Tremblay ML. Immunotherapeutic implications of negative regulation by protein tyrosine phosphatases in T cells: the emerging cases of PTP1B and TCPTP. Front Med (Lausanne) 2024; 11:1364778. [PMID: 38707187 PMCID: PMC11066278 DOI: 10.3389/fmed.2024.1364778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/27/2024] [Indexed: 05/07/2024] Open
Abstract
In the context of inflammation, T cell activation occurs by the concerted signals of the T cell receptor (TCR), co-stimulatory receptors ligation, and a pro-inflammatory cytokine microenvironment. Fine-tuning these signals is crucial to maintain T cell homeostasis and prevent self-reactivity while offering protection against infectious diseases and cancer. Recent developments in understanding the complex crosstalk between the molecular events controlling T cell activation and the balancing regulatory cues offer novel approaches for the development of T cell-based immunotherapies. Among the complex regulatory processes, the balance between protein tyrosine kinases (PTK) and the protein tyrosine phosphatases (PTPs) controls the transcriptional and metabolic programs that determine T cell function, fate decision, and activation. In those, PTPs are de facto regulators of signaling in T cells acting for the most part as negative regulators of the canonical TCR pathway, costimulatory molecules such as CD28, and cytokine signaling. In this review, we examine the function of two close PTP homologs, PTP1B (PTPN1) and T-cell PTP (TCPTP; PTPN2), which have been recently identified as promising candidates for novel T-cell immunotherapeutic approaches. Herein, we focus on recent studies that examine the known contributions of these PTPs to T-cell development, homeostasis, and T-cell-mediated immunity. Additionally, we describe the signaling networks that underscored the ability of TCPTP and PTP1B, either individually and notably in combination, to attenuate TCR and JAK/STAT signals affecting T cell responses. Thus, we anticipate that uncovering the role of these two PTPs in T-cell biology may lead to new treatment strategies in the field of cancer immunotherapy. This review concludes by exploring the impacts and risks that pharmacological inhibition of these PTP enzymes offers as a therapeutic approach in T-cell-based immunotherapies.
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Affiliation(s)
- Luis Alberto Perez-Quintero
- Rosalind and Morris Goodman Cancer Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Belma Melda Abidin
- Rosalind and Morris Goodman Cancer Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Michel L. Tremblay
- Rosalind and Morris Goodman Cancer Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
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Skoracka K, Hryhorowicz S, Tovoli F, Raiteri A, Rychter AM, Słomski R, Dobrowolska A, Granito A, Krela-Kaźmierczak I. From an understanding of etiopathogenesis to novel therapies-what is new in the treatment of celiac disease? Front Pharmacol 2024; 15:1378172. [PMID: 38698821 PMCID: PMC11063403 DOI: 10.3389/fphar.2024.1378172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Celiac disease, a chronic autoimmune disorder caused by genetic factors and exposure to gluten, is increasingly being recognized and diagnosed in both children and adults. Scientists have been searching for a cure for this disease for many years, but despite the impressive development of knowledge in this field, a gluten-free diet remains the only recommended therapy for all patients. At the same time, the increasing diagnosis of celiac disease in adults, which was considered a childhood disease in the 20th century, has opened a discussion on the etiopathology of the disease, which is proven to be very complex and involves genetic, immunological, nutritional, environmental and gut microbiota-related factors. In this review, we extensively discuss these factors and summarize the knowledge of the proposed state-of-the-art treatments for celiac disease to address the question of whether a better understanding of the etiopathogenesis of celiac disease has opened new directions for therapy.
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Affiliation(s)
- Kinga Skoracka
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Francesco Tovoli
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Alberto Raiteri
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Anna Maria Rychter
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Nutrigenetics, Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alessandro Granito
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Nutrigenetics, Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
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8
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Wang W, Huang M, Ge W, Feng J, Zhang X, Li C, Wang L. Identifying serum metabolite biomarkers for autoimmune diseases: a two-sample mendelian randomization and meta-analysis. Front Immunol 2024; 15:1300457. [PMID: 38686387 PMCID: PMC11056515 DOI: 10.3389/fimmu.2024.1300457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Background Extensive evidence suggests a link between alterations in serum metabolite composition and various autoimmune diseases (ADs). Nevertheless, the causal relationship underlying these correlations and their potential utility as dependable biomarkers for early AD detection remain uncertain. Objective The objective of this study was to employ a two-sample Mendelian randomization (MR) approach to ascertain the causal relationship between serum metabolites and ADs. Additionally, a meta-analysis incorporating data from diverse samples was conducted to enhance the validation of this causal effect. Materials and methods A two-sample MR analysis was performed to investigate the association between 486 human serum metabolites and six prevalent autoimmune diseases: systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), inflammatory bowel disease (IBD), dermatomyositis (DM), type 1 diabetes (T1D), and celiac disease (CeD). The inverse variance weighted (IVW) model was employed as the primary analytical technique for the two-sample MR analysis, aiming to identify blood metabolites linked with autoimmune diseases. Independent outcome samples were utilized for further validation of significant blood metabolites. Additional sensitivity analyses, including heterogeneity test, horizontal pleiotropy test, and retention rate analysis, were conducted. The results from these analyses were subsequently meta-integrated. Finally, metabolic pathway analysis was performed using the KEGG and Small Molecule Pathway Databases (SMPD). Results Following the discovery and replication phases, eight metabolites were identified as causally associated with various autoimmune diseases, encompassing five lipid metabolism types: 1-oleoylglycerophosphoethanolamine, 1-arachidonoylglycerophosphoethanolamine, 1-myristoylglycerophosphocholine, arachidonate (20:4 n6), and glycerol. The meta-analysis indicated that three out of these eight metabolites exhibited a protective effect, while the remaining five were designated as pathogenic factors. The robustness of these associations was further confirmed through sensitivity analysis. Moreover, an investigation into metabolic pathways revealed a significant correlation between galactose metabolism and autoimmune diseases. Conclusion This study revealed a causal relationship between lipid metabolites and ADs, providing novel insights into the mechanism of AD development mediated by serum metabolites and possible biomarkers for early diagnosis.
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Affiliation(s)
- Wenwen Wang
- Department of Health Statistics, School of Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Manli Huang
- Department of Health Statistics, School of Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Wei Ge
- Department of Field and Disaster Nursing, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Junling Feng
- Department of Health Statistics, School of Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xihua Zhang
- Department of Neurological Intensive Care Rehabilitation, Xi’an International Medical Center Hospital, Xi’an, Shaanxi, China
| | - Chen Li
- Department of Health Statistics, School of Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Ling Wang
- Department of Health Statistics, School of Preventive Medicine, Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi’an, Shaanxi, China
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Jeong R, Bulyk ML. Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases. bioRxiv 2024:2024.04.12.589213. [PMID: 38659802 PMCID: PMC11042205 DOI: 10.1101/2024.04.12.589213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Most genetic loci associated with complex traits and diseases through genome-wide association studies (GWAS) are noncoding, suggesting that the causal variants likely have gene regulatory effects. However, only a small number of loci have been linked to expression quantitative trait loci (eQTLs) detected currently. To better understand the potential reasons for many trait-associated loci lacking eQTL colocalization, we investigated whether chromatin accessibility QTLs (caQTLs) in lymphoblastoid cell lines (LCLs) explain immune-mediated disease associations that eQTLs in LCLs did not. The power to detect caQTLs was greater than that of eQTLs and was less affected by the distance from the transcription start site of the associated gene. Meta-analyzing LCL eQTL data to increase the sample size to over a thousand led to additional loci with eQTL colocalization, demonstrating that insufficient statistical power is still likely to be a factor. Moreover, further eQTL colocalization loci were uncovered by surveying eQTLs of other immune cell types. Altogether, insufficient power and context-specificity of eQTLs both contribute to the 'missing regulation.'
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Affiliation(s)
- Raehoon Jeong
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA 02138, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Bioinformatics and Integrative Genomics Graduate Program, Harvard University, Cambridge, MA 02138, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively parallel reporter assay confirms regulatory potential of hQTLs and reveals important variants in lupus and other autoimmune diseases. HGG Adv 2024; 5:100279. [PMID: 38389303 PMCID: PMC10943488 DOI: 10.1016/j.xhgg.2024.100279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele-dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared with other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies in primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships among genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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Maihofer AX, Ratanatharathorn A, Hemmings SMJ, Costenbader KH, Michopoulos V, Polimanti R, Rothbaum AO, Seedat S, Mikita EA, Smith AK, Salem RM, Shaffer RA, Wu T, Sebat J, Ressler KJ, Stein MB, Koenen KC, Wolf EJ, Sumner JA, Nievergelt CM. Effects of genetically predicted posttraumatic stress disorder on autoimmune phenotypes. Transl Psychiatry 2024; 14:172. [PMID: 38561342 PMCID: PMC10984931 DOI: 10.1038/s41398-024-02869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Observational studies suggest that posttraumatic stress disorder (PTSD) increases risk for various autoimmune diseases. Insights into shared biology and causal relationships between these diseases may inform intervention approaches to PTSD and co-morbid autoimmune conditions. We investigated the shared genetic contributions and causal relationships between PTSD, 18 autoimmune diseases, and 3 immune/inflammatory biomarkers. Univariate MiXeR was used to contrast the genetic architectures of phenotypes. Genetic correlations were estimated using linkage disequilibrium score regression. Bi-directional, two-sample Mendelian randomization (MR) was performed using independent, genome-wide significant single nucleotide polymorphisms; inverse variance weighted and weighted median MR estimates were evaluated. Sensitivity analyses for uncorrelated (MR PRESSO) and correlated horizontal pleiotropy (CAUSE) were also performed. PTSD was considerably more polygenic (10,863 influential variants) than autoimmune diseases (median 255 influential variants). However, PTSD evidenced significant genetic correlation with nine autoimmune diseases and three inflammatory biomarkers. PTSD had putative causal effects on autoimmune thyroid disease (p = 0.00009) and C-reactive protein (CRP) (p = 4.3 × 10-7). Inferences were not substantially altered by sensitivity analyses. Additionally, the PTSD-autoimmune thyroid disease association remained significant in multivariable MR analysis adjusted for genetically predicted inflammatory biomarkers as potential mechanistic pathway variables. No autoimmune disease had a significant causal effect on PTSD (all p values > 0.05). Although causal effect models were supported for associations of PTSD with CRP, shared pleiotropy was adequate to explain a putative causal effect of CRP on PTSD (p = 0.18). In summary, our results suggest a significant genetic overlap between PTSD, autoimmune diseases, and biomarkers of inflammation. PTSD has a putative causal effect on autoimmune thyroid disease, consistent with existing epidemiologic evidence. A previously reported causal effect of CRP on PTSD is potentially confounded by shared genetics. Together, results highlight the nuanced links between PTSD, autoimmune disorders, and associated inflammatory signatures, and suggest the importance of targeting related pathways to protect against disease and disability.
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Affiliation(s)
- Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA.
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.
| | - Andrew Ratanatharathorn
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- South African Medical Research Council/Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Karen H Costenbader
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vasiliki Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Renato Polimanti
- VA Connecticut Healthcare Center, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Alex O Rothbaum
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Research and Outcomes, Skyland Trail, Atlanta, GA, USA
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- South African Medical Research Council/Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elizabeth A Mikita
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Richard A Shaffer
- Department of Epidemiology and Health Sciences, Naval Health Research Center, San Diego, CA, USA
| | - Tianying Wu
- Division of Epidemiology and Biostatistics, School of Public Health, San Diego State University, San Diego, CA, USA
- Moores Cancer Center, University of California, San Diego, San Diego, CA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Erika J Wolf
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jennifer A Sumner
- Department of Psychology, University of California Los Angeles, Los Angeles, CA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
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12
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Wang ZL, Pang SJ, Zhang KW, Li PY, Li PG, Yang C. Dietary vitamin A modifies the gut microbiota and intestinal tissue transcriptome, impacting intestinal permeability and the release of inflammatory factors, thereby influencing Aβ pathology. Front Nutr 2024; 11:1367086. [PMID: 38606018 PMCID: PMC11008281 DOI: 10.3389/fnut.2024.1367086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
Background Alzheimer's disease (AD) is an age-related neurodegenerative disorder with no effective interventions for curing or modifying its progression. However, emerging research suggests that vitamin A in the diet may play a role in both the prevention and treatment of AD, although the exact mechanisms are not fully understood. Objectives This study aims to investigate the dietary vitamin A modifies the gut microbiota and intestinal tissue transcriptome, impacting intestinal permeability and the release of inflammatory factors, thereby influencing Aβ pathology shedding light on its potential as a dietary intervention for AD prevention and treatment. Methods The APP/PS1-AD mouse model was employed and divided into three dietary groups: vitamin A-deficient (VAD), normal vitamin A (VAN), and vitamin A-supplemented (VAS) for a 12-week study. Neurobehavioral functions were assessed using the Morris Water Maze Test (MWM). Enzyme-linked immunosorbent assay (ELISA) was used to quantify levels of Diamine Oxidase (DAO), D-lactate, IL-6, IL-1β, and TNF-a cytokines. Serum vitamin A levels were analyzed via LC-MS/MS analysis. Immunohistochemical analysis and morphometry were performed to evaluate the deposition of Aβ in brain tissue. The gut microbiota of APP/PS1 mice was analyzed using 16S rRNA sequencing analysis. Additionally, transcriptomic analysis was conducted on intestinal tissue from APP/PS1 mice. Results No significant changes in food intake and body weight were observed among the groups. However, the VAD and VAS groups showed reduced food intake compared to the VAN group at various time points. In terms of cognitive function, the VAN group performed better in the Morris Water Maze Test, indicating superior learning and memory abilities. The VAD and VAS groups exhibited impaired performance, with the VAS group performing relatively better than the VAD group. Serum vitamin A concentrations differed significantly among the groups, with the VAS group having the highest concentration. Aβ levels were significantly higher in the VAD group compared to both the VAN and VAS groups. Microbial analysis revealed that the VAS and VAN groups had higher microbial diversity than the VAD group, with specific taxa characterizing each group. The VAN group was characterized by taxa such as Actinohacteriota and Desulfovibrionaceae, while the VAD group was characterized by Parabacteroides and Tannerellaceae. The VAS group showed similarities with both VAN and VAD groups, with taxa like Desulfobacterota and Desulfovibrionaceae being present. The VAD vs. VAS, VAD vs. VAN, and VAS vs. VAN comparisons identified 571, 313, and 243 differentially expressed genes, respectively, which associated with cellular and metabolic processes, and pathway analysis revealed enrichment in pathways related to chemical carcinogenesis, drug metabolism, glutathione metabolism, and immune-related processes. The VAD group exhibited higher levels of D-lactate, diamine oxidase, and inflammatory cytokines (TNF-a, IL-1β, IL-6) compared to the VAN and VAS groups. Conclusion Dietary vitamin A supplementation modulates the gut microbiota, intestinal permeability, inflammatory factors, and Aβ protein formation, offering insights into the pathogenesis of AD and potential therapeutic avenues for further exploration. This research highlights the intricate interplay between diet, gut microbiota, and neurodegenerative processes, emphasizing the importance of dietary interventions in managing AD-related pathologies.
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Affiliation(s)
- Zhong-Li Wang
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Jiaxing University, The Second Hospital of Jiaxing, Zhejiang, China
| | - Shao-Jie Pang
- Heilongjiang Feihe Dairy Co., Ltd. Feihe Research Institute, Beijing, China
| | - Kai-Wen Zhang
- School of Public Health, Capital Medical University, Beijing, China
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peng-Yu Li
- School of Public Health, Capital Medical University, Beijing, China
| | - Peng-Gao Li
- School of Public Health, Capital Medical University, Beijing, China
| | - Chun Yang
- School of Public Health, Capital Medical University, Beijing, China
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13
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Yuan W, Li X, Wang G, Qu B, Zhao F. Association of autoimmune and allergic diseases with senile cataract: a bidirectional two-sample Mendelian randomization study. Front Immunol 2024; 15:1325868. [PMID: 38585265 PMCID: PMC10995295 DOI: 10.3389/fimmu.2024.1325868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
Background Many observational studies have been reported that patients with autoimmune or allergic diseases seem to have a higher risk of developing senile cataract, but the views are not consistent. In order to minimize the influence of reverse causality and potential confounding factors, we performed Mendelian Randomization (MR) analysis to investigate the genetic causal associations between autoimmune, allergic diseases and senile cataract. Methods Single nucleotide polymorphisms associated with ten common autoimmune and allergic diseases were obtained from the IEU Open genome-wide association studies (GWAS) database. Summary-level GWAS statistics for clinically diagnosed senile cataract were obtained from the FinnGen research project GWAS, which consisted of 59,522 individuals with senile cataracts and 312,864 control individuals. MR analysis was conducted using mainly inverse variance weighted (IVW) method and further sensitivity analysis was performed to test robustness. Results As for ten diseases, IVW results confirmed that type 1 diabetes (OR = 1.06; 95% CI = 1.05-1.08; p = 2.24×10-12), rheumatoid arthritis (OR = 1.05; 95% CI = 1.02-1.08; p = 1.83×10-4), hypothyroidism (OR = 2.4; 95% CI = 1.42-4.06; p = 1.12×10-3), systemic lupus erythematosus (OR = 1.02; 95% CI = 1.01-1.03; p = 2.27×10-3), asthma (OR = 1.02; 95% CI = 1.01-1.03; p = 1.2×10-3) and allergic rhinitis (OR = 1.07; 95% CI = 1.02-1.11; p = 2.15×10-3) were correlated with the risk of senile cataract. Celiac disease (OR = 1.04; 95% CI = 1.01-1.08; P = 0.0437) and atopic dermatitis (OR = 1.05; 95% CI = 1.01-1.10; P = 0.0426) exhibited a suggestive connection with senile cataract after Bonferroni correction. These associations are consistent across weighted median and MR Egger methods, with similar causal estimates in direction and magnitude. Sensitivity analysis further proved that these associations were reliable. Conclusions The results of the MR analysis showed that there were causal relationships between type 1 diabetes, rheumatoid arthritis, hypothyroidism, systemic lupus erythematosus, asthma, allergic rhinitis and senile cataract. To clarify the possible role of autoimmune and allergy in the pathophysiology of senile cataract, further studies are needed.
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Affiliation(s)
- Weichen Yuan
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Xiangrui Li
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Guan Wang
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Bo Qu
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Fangkun Zhao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
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Enduru N, Fernandes BS, Bahrami S, Dai Y, Andreassen OA, Zhao Z. Genetic overlap between Alzheimer's disease and immune-mediated diseases: an atlas of shared genetic determinants and biological convergence. Mol Psychiatry 2024:10.1038/s41380-024-02510-y. [PMID: 38499654 DOI: 10.1038/s41380-024-02510-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
The occurrence of immune disease comorbidities in Alzheimer's disease (AD) has been observed in both epidemiological and molecular studies, suggesting a neuroinflammatory basis in AD. However, their shared genetic components have not been systematically studied. Here, we composed an atlas of the shared genetic associations between 11 immune-mediated diseases and AD by analyzing genome-wide association studies (GWAS) summary statistics. Our results unveiled a significant genetic overlap between AD and 11 individual immune-mediated diseases despite negligible genetic correlations, suggesting a complex shared genetic architecture distributed across the genome. The shared loci between AD and immune-mediated diseases implicated several genes, including GRAMD1B, FUT2, ADAMTS4, HBEGF, WNT3, TSPAN14, DHODH, ABCB9, and TNIP1, all of which are protein-coding genes and thus potential drug targets. Top biological pathways enriched with these identified shared genes were related to the immune system and cell adhesion. In addition, in silico single-cell analyses showed enrichment of immune and brain cells, including neurons and microglia. In summary, our results suggest a genetic relationship between AD and the 11 immune-mediated diseases, pinpointing the existence of a shared however non-causal genetic basis. These identified protein-coding genes have the potential to serve as a novel path to therapeutic interventions for both AD and immune-mediated diseases and their comorbidities.
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Affiliation(s)
- Nitesh Enduru
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Brisa S Fernandes
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Shahram Bahrami
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Yulin Dai
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Zhongming Zhao
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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15
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Sha Y, Liu X, He Y, Zhao S, Hu J, Wang J, Li W, Shao P, Wang F, Chen X, Yang W, Xie Z. Multi-omics revealed rumen microbiota metabolism and host immune regulation in Tibetan sheep of different ages. Front Microbiol 2024; 15:1339889. [PMID: 38414776 PMCID: PMC10896911 DOI: 10.3389/fmicb.2024.1339889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/17/2024] [Indexed: 02/29/2024] Open
Abstract
The rumen microbiota and metabolites play an important role in energy metabolism and immune regulation of the host. However, the regulatory mechanism of rumen microbiota and metabolite interactions with host on Tibetan sheep's plateau adaptability is still unclear. We analyzed the ruminal microbiome and metabolome, host transcriptome and serum metabolome characteristics of Tibetan sheep at different ages. Biomarkers Butyrivibrio, Lachnospiraceae_XPB1014_group, Prevotella, and Rikenellaceae_RC9_gut_group were found in 4 months, 1.5 years, 3.5 years, and 6 years Tibetan sheep, respectively. The rumen microbial metabolites were mainly enriched in galactose metabolism, unsaturated fatty acid biosynthesis and fatty acid degradation pathways, and had significant correlation with microbiota. These metabolites further interact with mRNA, and are co-enriched in arginine and proline metabolism, metabolism of xenobiotics by cytochrome P450, propanoate metabolism, starch and sucrose metabolism, gap junction pathway. Meanwhile, serum metabolites also have a similar function, such as chemical carcinogenesis - reactive oxygen species, limonene and pinene degradation, and cutin, suberine and wax biosynthesis, thus participating in the regulation of the body's immune and energy-related metabolic processes. This study systematically revealed that rumen microbiota, metabolites, mRNA and serum metabolites of Tibetan sheep were involved in the regulation of fermentation metabolic function and immune level of Tibetan sheep at different ages, which provided a new perspective for plateau adaptability research of Tibetan sheep at different ages.
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Affiliation(s)
- Yuzhu Sha
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Shengguo Zhao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Wenhao Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Pengyang Shao
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Fanxiong Wang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Xiaowei Chen
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Yang
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
| | - Zhuanhui Xie
- College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou, China
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Størdal K, Tapia G, Lund-Blix NA, Stene LC. Genotypes predisposing for celiac disease and autoimmune diabetes and risk of infections in early childhood. J Pediatr Gastroenterol Nutr 2024; 78:295-303. [PMID: 38374560 DOI: 10.1002/jpn3.12078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 02/21/2024]
Abstract
OBJECTIVES Infections in early childhood have been associated with risk of celiac disease (CD) and type 1 diabetes (T1D). We investigated whether this is driven by susceptibility genes for autoimmune disease by comparing infection frequency by genetic susceptibility variants for CD or T1D. METHODS We genotyped 373 controls and 384 children who developed CD or T1D in the population-based Norwegian Mother, Father and Child Cohort study (MoBa) study for human leukocyte antigen (HLA)-DQ, FUT2, SH2B3, and PTPN22, and calculated a weighted non-HLA genetic risk score (GRS) for CD and T1D based on over 40 SNPs. Parents reported infections in questionnaires when children were 6 and 18 months old. We used negative binomial regression to estimate incidence rate ratio (IRR) for infections by genotype. RESULTS HLA genotypes for CD and T1D or non-HLA GRS for T1D were not associated with infections. The non-HLA GRS for CD was associated with a nonsignificantly lower frequency of infections (aIRR: 0.95, 95% CI: 0.87-1.03 per weighted allele score), and significantly so when restricting to healthy controls (aIRR: 0.89, 0.81-0.99). Participants homozygous for rs601338(A;A) at FUT2, often referred to as nonsecretors, had a nonsignificantly lower risk of infections (aIRR: 0.91, 95% CI: 0.83-1.01). SH2B3 and PTPN22 genotypes were not associated with infections. The association between infections and risk of CD (OR: 1.15 per five infections) was strengthened after adjustment for HLA genotype and non-HLA GRS (OR: 1.24). CONCLUSIONS HLA variants and non-HLA GRS conferring susceptibility for CD were not associated with increased risk of infections in early childhood and is unlikely to drive the observed association between infections and risk of CD or T1D in many studies.
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Affiliation(s)
- Ketil Størdal
- Department of Pediatric Research, Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - German Tapia
- Norwegian Institute of Public Health, Oslo, Norway
| | | | - Lars C Stene
- Norwegian Institute of Public Health, Oslo, Norway
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Banerjee P, Sood A, Midha V, Narang V, Grover J, Senapati S. A duodenal mucosa transcriptome study identified reduced expression of a novel gene CDH18 in celiac disease. Dig Liver Dis 2024; 56:258-264. [PMID: 37813809 DOI: 10.1016/j.dld.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Celiac disease (CD) a complex immune disease that affects duodenal mucosa. Identification of tissue specific biomarkers is expected to improve the existing biopsy based CD diagnosis. AIMS To investigate the differentially expressed genes (DEGs) in duodenal mucosa tissue to identify clinically relevant gene expression pattern in CD. METHODS Whole RNA extracted from the duodenal biopsies of three CD patients and four non-CD controls were sequenced. Significant DEGs were identified. Prioritized DEGs were validated using qRT-PCR in an independent group (CD=23; Control=26). Enriched pathways were analyzed, protein-protein interaction networks were evaluated. RESULTS 923 DEGs comprising of 135 up-regulated, and 788 down-regulated genes, with p-value≤0.05; log2FC>2 or <-2 were identified. A novel down-regulated gene CDH18 (p = 0.03; log2FC=-0.74) was identified. Previously known CXCL9 was replicated. CDH18, a trans-membrane protein was found to interact with other CDH proteins, α/β catenins, and other membrane transporters such as SLC and ABCB. Pathways and protein networks contributing in channel activity (p = 2.15E-12), membrane transporters (p = 2.15E-12), and cellular adhesion (p = 8.05E-6) were identified. CONCLUSIONS CDH18, a novel DEG identified in the present study is a pivotal gene involved in maintaining epithelial membrane organization and integrity. The functional significance of lower expression of CDH18 in pathogenesis of CD warranted to be investigated. CDH18 expression could be tested for its effectiveness in diagnostic, prognostic and therapeutic purposes.
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Affiliation(s)
- Pratibha Banerjee
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, Punjab, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Vandana Midha
- Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Vikram Narang
- Department of Pathology, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Jasmine Grover
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141001, Punjab, India
| | - Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, Punjab, India.
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Wang L, Wang X, Wang T. Effects of increasing drip irrigation at different maize growth stages on soil microorganisms. Front Microbiol 2024; 15:1343302. [PMID: 38357342 PMCID: PMC10864578 DOI: 10.3389/fmicb.2024.1343302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction To investigate the effects of different drip irrigation periods on soil microbial communities and functions. Methods Increasing drip irrigation amount at the seedling (S), jointing (J), bell (B), tasseling (T) and grain filling (G) stages of maize were studied using no increase in irrigation amount as control (CK). Principal component analysis was conducted to comprehensively evaluate soil microbial quality following the different drip irrigation treatments. In addition, the characteristics of the community structure and the potential functional composition of soil bacteria and fungi were comparatively analyzed by combining amplicon sequencing and functional prediction methods. Results The results indicated that MBNT15 was the most important genus for the classification of soil bacterial samples, Saitozyma was the most important genus for the classification of soil fungal samples, and fungi were more important than bacteria for the classification of soil microbial samples. Compared with fungal communities, bacterial communities exhibited high levels of functional diversity. The proportion of metabolism was the highest in the prediction of bacterial primary functions, and carbohydrate metabolism and amino acid metabolism were important functions in the prediction of bacterial secondary functions. BugBase phenotype prediction results showed that soil bacteria under B treatment had a higher number of aerobic bacteria and greater resistance to disease and stress. The J treatment had the highest number of bacteria with biofilm forms, and the J, S, and G treatments contained more potentially pathogenic bacteria but fewer stress-tolerant bacteria compared with the CK treatment. The number of Saprotroph was the largest and the number of Symbiotroph was the least. The relative abundances of Saprotroph, Pathotroph and Symbiotroph were 68.60%~74.33%, 15.76%~20.60% and 9.16%~11.13%, respectively. Discussion The findings provide a reference for conserving water resources, improving maize yield, and predicting soil microbial metabolic potential and function by reflecting the richness of the soil microbial community structure in maize fields.
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Affiliation(s)
- Lei Wang
- Shanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan, Shanxi, China
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Xiaojuan Wang
- Shanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan, Shanxi, China
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
- State Key Laboratory of Integrative Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan, Shanxi, China
- Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry of Agriculture and Rural Affairs and Shanxi Province), Shanxi Agricultural University, Taiyuan, Shanxi, China
- Shanxi Province Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Tianle Wang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
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Shi X, Wallach JD, Ma X, Rogne T. Autoimmune diseases and risk of non-Hodgkin lymphoma: A Mendelian randomisation study. medRxiv 2024:2024.01.20.24301459. [PMID: 38343812 PMCID: PMC10854352 DOI: 10.1101/2024.01.20.24301459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Objective To examine whether genetically predicted susceptibility to ten autoimmune diseases (Behçet's disease, coeliac disease, dermatitis herpetiformis, lupus, psoriasis, rheumatoid arthritis, sarcoidosis, Sjögren's syndrome, systemic sclerosis, and type 1 diabetes) is associated with risk of non-Hodgkin lymphoma (NHL). Design Two sample Mendelian randomization (MR) study. Setting Genome wide association studies (GWASs) of ten autoimmune diseases, NHL, and four NHL subtypes (i.e., follicular lymphoma, mature T/natural killer-cell lymphomas, non-follicular lymphoma, and other and unspecified types of NHL). Analysis We used data from the largest publicly available GWASs of European ancestry for each autoimmune disease, NHL, and NHL subtypes. For each autoimmune disease, we extracted single nucleotide polymorphisms (SNPs) strongly associated (P < 5×10-8) with that disease and that were independent of one another (R2 < 1×10-3) as genetic instruments. SNPs within the human leukocyte antigen region were not considered due to potential pleiotropy. Our primary MR analysis was the inverse-variance weighted analysis. Additionally, we conducted MR-Egger, weighted mode, and weighted median regression to address potential bias due to pleiotropy, and robust adjusted profile scores to address weak instrument bias. We carried out sensitivity analysis limited to the non-immune pathway for nominally significant findings. To account for multiple testing, we set the thresholds for statistical significance at P < 5×10-3. Participants The number of cases and controls identified in the relevant GWASs were 437 and 3,325 for Behçet's disease, 4,918 and 5,684 for coeliac disease, 435 and 341,188 for dermatitis herpetiformis, 4,576 and 8,039 for lupus, 11,988 and 275,335 for psoriasis, 22,350 and 74,823 for rheumatoid arthritis, 3,597 and 337,121 for sarcoidosis, 2,735 and 332,115 for Sjögren's syndrome, 9,095 and 17,584 for systemic sclerosis, 18,942 and 501,638 for type 1 diabetes, 2,400 and 410,350 for NHL; and 296 to 2,340 cases and 271,463 controls for NHL subtypes. Exposures Genetic variants predicting ten autoimmune diseases: Behçet's disease, coeliac disease, dermatitis herpetiformis, lupus, psoriasis, rheumatoid arthritis, sarcoidosis, Sjögren's syndrome, systemic sclerosis, and type 1 diabetes. Main outcome measures Estimated associations between genetically predicted susceptibility to ten autoimmune diseases and the risk of NHL. Results The variance of each autoimmune disease explained by the SNPs ranged from 0.3% to 3.1%. Negative associations between type 1 diabetes and sarcoidosis and the risk of NHL were observed (odds ratio [OR] 0.95, 95% confidence interval [CI]: 0.92 to 0.98, P = 5×10-3, and OR 0.92, 95% CI: 0.85 to 0.99, P = 2.8×10-2, respectively). These findings were supported by the sensitivity analyses accounting for potential pleiotropy and weak instrument bias. No significant associations were found between the other eight autoimmune diseases and NHL risk. Of the NHL subtypes, type 1 diabetes was most strongly associated with follicular lymphoma (OR 0.91, 95% CI: 0.86 to 0.96, P = 1×10-3), while sarcoidosis was most strongly associated with other and unspecified NHL (OR 0.86, 95% CI: 0.75 to 0.97, P = 1.8×10-2). Conclusions These findings suggest that genetically predicted susceptibility to type 1 diabetes, and to some extent sarcoidosis, might reduce the risk of NHL. However, future studies with different datasets, approaches, and populations are warranted to further examine the potential associations between these autoimmune diseases and the risk of NHL.
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Affiliation(s)
- Xiaoting Shi
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Joshua D. Wallach
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Xiaomei Ma
- Department of Chronic Diseases Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Tormod Rogne
- Department of Chronic Diseases Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
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Alom MS, Cen Y, Tang R, Chen D, Dou H, Mo Z, Du H. Change of termite hindgut metabolome and bacteria after captivity indicates the hindgut microbiota provides nutritional factors to the host. Front Bioeng Biotechnol 2024; 11:1228918. [PMID: 38288244 PMCID: PMC10823432 DOI: 10.3389/fbioe.2023.1228918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/01/2023] [Indexed: 01/31/2024] Open
Abstract
The gut-dwelling microbiota is an indispensable part of termites. It is influenced by a series of factors, such as diet and captivity. The objectives of this study were to study the metabolic functions of hindgut microbiota and to investigate the influence of captivity on the hindgut microbiota. The dampwood termite Hodotermopsis sjostedti was reared in the laboratory for 6 months. We conducted the metabolome analysis of the fat body from the freshly-collected workers (FBF), the hindgut fluid of the freshly-collected workers (HFF), and the hindgut fluid of laboratory-maintained workers. In addition, the 16S rRNA genes from the hindgut bacteria in the freshly-collected and laboratory-maintained workers were sequenced. According to our results, the concentrations of metabolites associated with amino acid biosynthesis, vitamin biosynthesis, fatty acid biosynthesis, and cofactor biosynthesis were higher in HFF compared with those in FBF, suggesting that the hindgut microbiota provides nutritional factors to the host. However, after captivity, the concentrations of metabolites in the hindgut associated with amino acid biosynthesis, nucleotide sugar metabolism, vitamin biosynthesis, and carbon metabolism decreased, while those associated with the steroid hormone biosynthesis and ovarian steroidogenesis increased. Meanwhile, the 16S amplicon study revealed that the abundance of certain bacteria changed after captivity, such as uncultured Termite Group 1 bacterium, Candidatus Symbiothrix dinenymphae, and unclassified Desulfovibrio. Our findings show that captivity influences the hindgut microbiota and shed light on the metabolic potential of the hindgut microbiota.
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Affiliation(s)
- Most Shormi Alom
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yijing Cen
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Rui Tang
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Dasong Chen
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Hongliang Dou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Zhenzuan Mo
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - He Du
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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21
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Wang Y, Yang Y, Jia X, Zhao C, Yang C, Fan J, Wang N, Shi X. Identification of the shared genetic architecture underlying seven autoimmune diseases with GWAS summary statistics. Front Immunol 2024; 14:1303675. [PMID: 38259487 PMCID: PMC10800382 DOI: 10.3389/fimmu.2023.1303675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Background The common clinical symptoms and immunopathological mechanisms have been observed among multiple autoimmune diseases (ADs), but the shared genetic etiology remains unclear. Methods GWAS summary statistics of seven ADs were downloaded from Open Targets Genetics and Dryad. Linkage disequilibrium score regression (LDSC) was applied to estimate overall genetic correlations, bivariate causal mixture model (MiXeR) was used to qualify the polygenic overlap, and stratified-LDSC partitioned heritability to reveal tissue and cell type specific enrichments. Ultimately, we conducted a novel adaptive association test called MTaSPUsSet for identifying pleiotropic genes. Results The high heritability of seven ADs ranged from 0.1228 to 0.5972, and strong genetic correlations among certain phenotypes varied between 0.185 and 0.721. There was substantial polygenic overlap, with the number of shared SNPs approximately 0.03K to 0.21K. The specificity of SNP heritability was enriched in the immune/hematopoietic related tissue and cells. Furthermore, we identified 32 pleiotropic genes associated with seven ADs, 23 genes were considered as novel genes. These genes were involved in several cell regulation pathways and immunologic signatures. Conclusion We comprehensively explored the shared genetic architecture across seven ADs. The findings progress the exploration of common molecular mechanisms and biological processes involved, and facilitate understanding of disease etiology.
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Affiliation(s)
| | | | | | | | | | | | | | - Xuezhong Shi
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
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Stahl M, Koletzko S, Andrén Aronsson C, Lindfors K, Liu E, Agardh D. Coeliac disease: what can we learn from prospective studies about disease risk? Lancet Child Adolesc Health 2024; 8:63-74. [PMID: 37972632 PMCID: PMC10965251 DOI: 10.1016/s2352-4642(23)00232-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023]
Abstract
Paediatric prospective studies of coeliac disease with longitudinal collection of biological samples and clinical data offer a unique perspective on disease risk. This Review highlights the information now available from international paediatric prospective studies on genetic and environmental risk factors for coeliac disease. In addition, recent omics studies have made it possible to study complex interactions between genetic and environmental factors and thereby further our insight into the causes of the disease. In the future, paediatric prospective studies will be able to provide more detailed risk prediction models combining genes, the environment, and biological corroboration from multiomics. Such studies could also contribute to biomarker development and an improved understanding of disease pathogenesis.
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Affiliation(s)
- Marisa Stahl
- Pediatric Gastroenterology, Hepatology, and Nutrition, Digestive Health Institute, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Sibylle Koletzko
- Department of Pediatrics, Dr von Hauner Kinderspital, LMU University Hospital, LMU Munich, Munich, Germany; Department of Pediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum University of Warmia and Mazury, Olsztyn, Poland
| | - Carin Andrén Aronsson
- Unit of Celiac Disease and Diabetes, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Katri Lindfors
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Edwin Liu
- Pediatric Gastroenterology, Hepatology, and Nutrition, Digestive Health Institute, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Daniel Agardh
- Unit of Celiac Disease and Diabetes, Department of Clinical Sciences, Lund University, Malmö, Sweden
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Hernangomez-Laderas A, Cilleros-Portet A, Martínez Velasco S, Marí S, Legarda M, González-García BP, Tutau C, García-Santisteban I, Irastorza I, Fernandez-Jimenez N, Bilbao JR. Sex bias in celiac disease: XWAS and monocyte eQTLs in women identify TMEM187 as a functional candidate gene. Biol Sex Differ 2023; 14:86. [PMID: 38072919 PMCID: PMC10712119 DOI: 10.1186/s13293-023-00572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Celiac disease (CeD) is an immune-mediated disorder that develops in genetically predisposed individuals upon gluten consumption. HLA risk alleles explain 40% of the genetic component of CeD, so there have been continuing efforts to uncover non-HLA loci that can explain the remaining heritability. As in most autoimmune disorders, the prevalence of CeD is significantly higher in women. Here, we investigated the possible involvement of the X chromosome on the sex bias of CeD. METHODS We performed a X chromosome-wide association study (XWAS) and a gene-based association study in women from the CeD Immunochip (7062 cases, 5446 controls). We also constructed a database of X chromosome cis-expression quantitative trait loci (eQTLs) in monocytes from unstimulated (n = 226) and lipopolysaccharide (LPS)-stimulated (n = 130) female donors and performed a Summary-data-based MR (SMR) analysis to integrate XWAS and eQTL information. We interrogated the expression of the potentially causal gene (TMEM187) in peripheral blood mononuclear cells (PBMCs) from celiac patients at onset, on a gluten-free diet, potential celiac patients and non-celiac controls. RESULTS The XWAS and gene-based analyses identified 13 SNPs and 25 genes, respectively, 22 of which had not been previously associated with CeD. The X chromosome cis-eQTL analysis found 18 genes with at least one cis-eQTL in naïve female monocytes and 8 genes in LPS-stimulated female monocytes, 2 of which were common to both situations and 6 were unique to LPS stimulation. SMR identified a potentially causal association of TMEM187 expression in naïve monocytes with CeD in women, regulated by CeD-associated, eQTL-SNPs rs7350355 and rs5945386. The CeD-risk alleles were correlated with lower TMEM187 expression. These results were replicated using eQTLs from LPS-stimulated monocytes. We observed higher levels of TMEM187 expression in PBMCs from female CeD patients at onset compared to female non-celiac controls, but not in male CeD individuals. CONCLUSION Using X chromosome genotypes and gene expression data from female monocytes, SMR has identified TMEM187 as a potentially causal candidate in CeD. Further studies are needed to understand the implication of the X chromosome in the higher prevalence of CeD in women.
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Affiliation(s)
- Alba Hernangomez-Laderas
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Silvia Martínez Velasco
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Sergi Marí
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - María Legarda
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Bárbara Paola González-García
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Carlos Tutau
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
| | - Iñaki Irastorza
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain
- Pediatric Gastroenterology Unit, Cruces University Hospital, Barakaldo, Basque Country, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Basque Country, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
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Arenella M, Fanelli G, Kiemeney LA, McAlonan G, Murphy DG, Bralten J. Genetic relationship between the immune system and autism. Brain Behav Immun Health 2023; 34:100698. [PMID: 38020478 PMCID: PMC10663755 DOI: 10.1016/j.bbih.2023.100698] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Autism spectrum disorder (ASD) is a common and complex neurodevelopmental condition. The pathophysiology of ASD is poorly defined; however, it includes a strong genetic component and there is increasing evidence to support a role of immune dysregulation. Nonetheless, it is unclear which immune phenotypes link to ASD through genetics. Hence, we investigated the genetic correlation between ASD and diverse classes of immune conditions and markers; and if these immune-related genetic factors link to specific autistic-like traits in the population. We estimated global and local genetic correlations between ASD (n = 55,420) and 11 immune phenotypes (n = 14,256-755,406) using genome-wide association study summary statistics. Subsequently, polygenic scores (PGS) for these immune phenotypes were calculated in a population-based sample (n = 2487) and associated to five autistic-like traits (i.e., attention to detail, childhood behaviour, imagination, rigidity, social skills), and a total autistic-like traits score. Sex-stratified PGS analyses were also performed. At the genome-wide level, ASD was positively correlated with allergic diseases (ALG), and negatively correlated with lymphocyte count, rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE) (FDR-p = 0.01-0.02). At the local genetic level, ASD was correlated with RA, C-reactive protein, and granulocytes and lymphocyte counts (p = 5.8 × 10-6-0.002). In the general population sample, increased genetic liability for SLE, RA, ALG, and lymphocyte levels, captured by PGS, was associated with the total autistic score and with rigidity and childhood behaviour (FDR-p = 0.03). In conclusion, we demonstrated a genetic relationship between ASD and immunity that depends on the type of immune phenotype considered; some increase likelihood whereas others may potentially help build resilience. Also, this relationship may be restricted to specific genetic loci and link to specific autistic dimensions (e.g., rigidity).
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Affiliation(s)
- Martina Arenella
- Department of Forensic and Neurodevelopmental Science, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Giuseppe Fanelli
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Lambertus A. Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Grainne McAlonan
- Department of Forensic and Neurodevelopmental Science, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Maudsley and South London NHS Foundation, London, United Kingdom
| | - Declan G. Murphy
- Department of Forensic and Neurodevelopmental Science, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Maudsley and South London NHS Foundation, London, United Kingdom
| | - Janita Bralten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
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Gautam N, Wojciech L, Yap J, Chua YL, Ding EM, Sim DC, Tan AS, Ahl PJ, Prasad M, Tung DW, Connolly JE, Adriani G, Brzostek J, Gascoigne NR. Themis controls T cell activation, effector functions, and metabolism of peripheral CD8 + T cells. Life Sci Alliance 2023; 6:e202302156. [PMID: 37739454 PMCID: PMC10517225 DOI: 10.26508/lsa.202302156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023] Open
Abstract
Themis is important in regulating positive selection of thymocytes during T cell development, but its role in peripheral T cells is less understood. Here, we investigated T cell activation and its sequelae using a tamoxifen-mediated, acute Themis deletion mouse model. We find that proliferation, effector functions including anti-tumor killing, and up-regulation of energy metabolism are severely compromised. This study reveals the phenomenon of peripheral adaptation to loss of Themis, by demonstrating direct TCR-induced defects after acute deletion of Themis that were not evident in peripheral T cells chronically deprived of Themis in dLck-Cre deletion model. Peripheral adaptation to long-term loss was compared using chronic versus acute tamoxifen-mediated deletion and with the (chronic) dLck-Cre deletion model. We found that upon chronic tamoxifen-mediated Themis deletion, there was modulation in the gene expression profile for both TCR and cytokine signaling pathways. This profile overlapped with (chronic) dLck-Cre deletion model. Hence, we found that peripheral adaptation induced changes to both TCR and cytokine signaling modules. Our data highlight the importance of Themis in the activation of CD8+ T cells.
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Affiliation(s)
- Namrata Gautam
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lukasz Wojciech
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jiawei Yap
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yen Leong Chua
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Eyan Mw Ding
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Don Cn Sim
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alrina Sm Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Patricia J Ahl
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mukul Prasad
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Desmond Wh Tung
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - John E Connolly
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Giulia Adriani
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Joanna Brzostek
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nicholas Rj Gascoigne
- https://ror.org/01tgyzw49 Translational Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- https://ror.org/01tgyzw49 Translational Cancer Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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26
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Butler-Laporte G, Farjoun J, Nakanishi T, Lu T, Abner E, Chen Y, Hultström M, Metspalu A, Milani L, Mägi R, Nelis M, Hudjashov G, Yoshiji S, Ilboudo Y, Liang KYH, Su CY, Willet JDS, Esko T, Zhou S, Forgetta V, Taliun D, Richards JB. HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases. Commun Biol 2023; 6:1113. [PMID: 37923823 PMCID: PMC10624861 DOI: 10.1038/s42003-023-05496-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
The human leukocyte antigen (HLA) region on chromosome 6 is strongly associated with many immune-mediated and infection-related diseases. Due to its highly polymorphic nature and complex linkage disequilibrium patterns, traditional genetic association studies of single nucleotide polymorphisms do not perform well in this region. Instead, the field has adopted the assessment of the association of HLA alleles (i.e., entire HLA gene haplotypes) with disease. Often based on genotyping arrays, these association studies impute HLA alleles, decreasing accuracy and thus statistical power for rare alleles and in non-European ancestries. Here, we use whole-exome sequencing (WES) from 454,824 UK Biobank (UKB) participants to directly call HLA alleles using the HLA-HD algorithm. We show this method is more accurate than imputing HLA alleles and harness the improved statistical power to identify 360 associations for 11 auto-immune phenotypes (at least 129 likely novel), leading to better insights into the specific coding polymorphisms that underlie these diseases. We show that HLA alleles with synonymous variants, often overlooked in HLA studies, can significantly influence these phenotypes. Lastly, we show that HLA sequencing may improve polygenic risk scores accuracy across ancestries. These findings allow better characterization of the role of the HLA region in human disease.
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada.
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Joseph Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Tianyuan Lu
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Erik Abner
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mari Nelis
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Georgi Hudjashov
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Satoshi Yoshiji
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Yann Ilboudo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Kevin Y H Liang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Julian D S Willet
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Daniel Taliun
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- Department of Twin Research, King's College London, London, UK
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
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27
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Garrett-Sinha LA. An update on the roles of transcription factor Ets1 in autoimmune diseases. WIREs Mech Dis 2023; 15:e1627. [PMID: 37565573 PMCID: PMC10842644 DOI: 10.1002/wsbm.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Transcription factors are crucial to regulate gene expression in immune cells and in other cell types. In lymphocytes, there are a large number of different transcription factors that are known to contribute to cell differentiation and the balance between quiescence and activation. One such transcription factor is E26 oncogene homolog 1 (Ets1). Ets1 expression is high in quiescent B and T lymphocytes and its levels are decreased upon activation. The human ETS1 gene has been identified as a susceptibility locus for many autoimmune and inflammatory diseases. In accord with this, gene knockout of Ets1 in mice leads to development of a lupus-like autoimmune disease, with enhanced activation and differentiation of both B cells and T cells. Prior reviews have summarized functional roles for Ets1 based on studies of Ets1 knockout mice. In recent years, numerous additional studies have been published that further validate ETS1 as a susceptibility locus for human diseases where immune dysregulation plays a causative role. In this update, new information that further links Ets1 to human autoimmune diseases is organized and collated to serve as a resource. This update also describes recent studies that seek to understand molecularly how Ets1 regulates immune cell activation, either using human cells and tissues or mouse models. This resource is expected to be useful to investigators seeking to understand how Ets1 may regulate the human immune response, particularly in terms of its roles in autoimmunity and inflammation. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Lee Ann Garrett-Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York, USA
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28
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Pandey R, Bakay M, Hakonarson H. SOCS-JAK-STAT inhibitors and SOCS mimetics as treatment options for autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis. Front Immunol 2023; 14:1271102. [PMID: 38022642 PMCID: PMC10643230 DOI: 10.3389/fimmu.2023.1271102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Autoimmune diseases arise from atypical immune responses that attack self-tissue epitopes, and their development is intricately connected to the disruption of the JAK-STAT signaling pathway, where SOCS proteins play crucial roles. Conditions such as autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis exhibit immune system dysfunctions associated with JAK-STAT signaling dysregulation. Emerging therapeutic strategies utilize JAK-STAT inhibitors and SOCS mimetics to modulate immune responses and alleviate autoimmune manifestations. Although more research and clinical studies are required to assess their effectiveness, safety profiles, and potential for personalized therapeutic approaches in autoimmune conditions, JAK-STAT inhibitors and SOCS mimetics show promise as potential treatment options. This review explores the action, effectiveness, safety profiles, and future prospects of JAK inhibitors and SOCS mimetics as therapeutic agents for psoriasis, autoimmune uveitis, systemic lupus erythematosus, and autoimmune encephalitis. The findings underscore the importance of investigating these targeted therapies to advance treatment options for individuals suffering from autoimmune diseases.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA, United States
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29
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Fernandes B, Enduru N, Fernandes B, Bahrami S, Dai Y, Andreassen O, Zhao Z. Genetic overlap between Alzheimer's disease and immune-mediated diseases: An atlas of shared genetic determinants and biological convergence. Res Sq 2023:rs.3.rs-3346282. [PMID: 37841839 PMCID: PMC10571609 DOI: 10.21203/rs.3.rs-3346282/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The occurrence of immune disease comorbidities in Alzheimer's disease (AD) has been observed in both epidemiological and molecular studies, suggesting a neuroinflammatory basis in AD. However, their shared genetic components have not been systematically studied. Here, we composed an atlas of the shared genetic associations between 11 immune-mediated diseases and AD by analyzing genome-wide association studies (GWAS) summary statistics. Our results unveiled a significant genetic overlap between AD and 11 individual immune-mediated diseases despite negligible genetic correlations, suggesting a complex shared genetic architecture distributed across the genome. The shared loci between AD and immune-mediated diseases implicated several genes, including GRAMD1B, FUT2, ADAMTS4, HBEGF, WNT3, TSPAN14, DHODH, ABCB9 and TNIP1, all of which are protein-coding genes and thus potential drug targets. Top biological pathways enriched with these identified shared genes were related to the immune system and cell adhesion. In addition, in silico single-cell analyses showed enrichment of immune and brain cells, including neurons and microglia. In summary, our results suggest a genetic relationship between AD and the 11 immune-mediated diseases, pinpointing the existence of a shared however non-causal genetic basis. These identified protein-coding genes have the potential to serve as a novel path to therapeutic interventions for both AD and immune-mediated diseases and their comorbidities.
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Affiliation(s)
| | | | | | | | - Yulin Dai
- The University of Texas Health Science Center at Houston
| | - Ole Andreassen
- Oslo University Hospital & Institute of Clinical Medicine, University of Oslo
| | - Zhongming Zhao
- The University of Texas Health Science Center at Houston
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30
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Risemberg EL, Smeekens JM, Cisneros MCC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, de Villena FPM, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice. bioRxiv 2023:2023.09.13.557467. [PMID: 37745496 PMCID: PMC10515941 DOI: 10.1101/2023.09.13.557467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, unlike C3H/HeJ (C3H) mice. Objective To determine the genetic basis of orally-induced anaphylaxis to peanut in CC027 mice. Methods A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 and five additional CC strains. Results Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis, and 4% having severe anaphylaxis. A total of eight genetic loci were associated with variation in response to peanut challenge, six associated with anaphylaxis (temperature decrease) and two associated with peanut-specific IgE levels. There were two major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis (thymocyte-expressed molecule involved in selection) gene. Consistent with Themis' described functions, we found that CC027 have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. Conclusion Our results demonstrate a key role for Themis in the orally-reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L. Risemberg
- Curriculum in Bioinformatics and Computational Biology, UNC Chapel Hill
- Department of Genetics, UNC Chapel Hill
| | - Johanna M. Smeekens
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Marta C. Cruz Cisneros
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | - Brea K. Hampton
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | | | | | | | - Kelly Orgel
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Ginger D. Shaw
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | | | - A. Wesley Burks
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - William Valdar
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | - Michael D. Kulis
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
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31
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Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ. A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology. Nat Commun 2023; 14:5023. [PMID: 37596262 PMCID: PMC10439125 DOI: 10.1038/s41467-023-40679-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/07/2023] [Indexed: 08/20/2023] Open
Abstract
Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.
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Affiliation(s)
- Parsa Akbari
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- Medical Research Council Biostatistics Unit, University of Cambridge, East Forvie Building, Cambridge Biomedical Campus, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Dragana Vuckovic
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Luca Stefanucci
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Tao Jiang
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Kousik Kundu
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Roman Kreuzhuber
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Janine H Collins
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- Department of Haematology, Barts Health National Health Service Trust, London, E1 1BB, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Luigi Grassi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Institute for Health and Care Research Cambridge BioResource, Box 229, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jose A Guerrero
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Stephen Kaptoge
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Stuart Meacham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer Sambrook
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Institute for Health and Care Research Cambridge BioResource, Box 229, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Denis Seyres
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Institute for Health and Care Research Cambridge BioResource, Box 229, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Klaudia Walter
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Nicholas A Watkins
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - David J Roberts
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Headley Way, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Oxford Biomedical Research Centre-Haematology Theme, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- National Health Service Blood and Transplant, Oxford Centre, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
- Health Data Science Research Centre, Fondazione Human Technopole, Viale Rita Levi Montalcini 1, Milan, 20157, Italy
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, RILD Building, Barrack Road, Exeter, EX2 5DW, UK
| | - Stephen Burgess
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Medical Research Council Biostatistics Unit, University of Cambridge, East Forvie Building, Cambridge Biomedical Campus, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, CB2 0PT, UK
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Sanquin, University of Amsterdam, Amsterdam, Netherlands
| | - James E Peters
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Immunology and Inflammation, Imperial College London, Commonwealth Building, The Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
- Department of Haematology, University College London Hospitals, WC1E 6AS, London, UK.
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Genomics Research Centre, Fondazione Human Technopole, Viale Rita Levi Montalcini 1, Milan, 20157, Italy.
| | - William J Astle
- Medical Research Council Biostatistics Unit, University of Cambridge, East Forvie Building, Cambridge Biomedical Campus, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK.
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases. bioRxiv 2023:2023.08.17.553722. [PMID: 37645944 PMCID: PMC10462090 DOI: 10.1101/2023.08.17.553722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Objective To systematically characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate gene expression in an allele dependent manner. Methods We designed a massively parallel reporter assay (MPRA) containing ~32K variants and transfected it into an Epstein-Barr virus transformed B cell line generated from an SLE case. Results Our study expands our understanding of hQTLs, illustrating that epigenetic QTLs are more likely to contribute to functional mechanisms than eQTLs and other variant types, and a large proportion of hQTLs overlap transcription start sites (TSS) of noncoding RNAs. In addition, we nominate 17 variants (including 11 novel) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies primary and immortalized B cells. Conclusion We uncover important insights into the mechanistic relationships between genotype, epigenetics, gene expression, and SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
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Jalan A, Jayasree PJ, Karemore P, Narayan KP, Khandelia P. Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease. Mol Biotechnol 2023:10.1007/s12033-023-00792-1. [PMID: 37341888 DOI: 10.1007/s12033-023-00792-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
Cellular RNAs, both coding and noncoding are adorned by > 100 chemical modifications, which impact various facets of RNA metabolism and gene expression. Very often derailments in these modifications are associated with a plethora of human diseases. One of the most oldest of such modification is pseudouridylation of RNA, wherein uridine is converted to a pseudouridine (Ψ) via an isomerization reaction. When discovered, Ψ was referred to as the 'fifth nucleotide' and is chemically distinct from uridine and any other known nucleotides. Experimental evidence accumulated over the past six decades, coupled together with the recent technological advances in pseudouridine detection, suggest the presence of pseudouridine on messenger RNA, as well as on diverse classes of non-coding RNA in human cells. RNA pseudouridylation has widespread effects on cellular RNA metabolism and gene expression, primarily via stabilizing RNA conformations and destabilizing interactions with RNA-binding proteins. However, much remains to be understood about the RNA targets and their recognition by the pseudouridylation machinery, the regulation of RNA pseudouridylation, and its crosstalk with other RNA modifications and gene regulatory processes. In this review, we summarize the mechanism and molecular machinery involved in depositing pseudouridine on target RNAs, molecular functions of RNA pseudouridylation, tools to detect pseudouridines, the role of RNA pseudouridylation in human diseases like cancer, and finally, the potential of pseudouridine to serve as a biomarker and as an attractive therapeutic target.
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Affiliation(s)
- Abhishek Jalan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - P J Jayasree
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Pragati Karemore
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Kumar Pranav Narayan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India.
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Yin Q, Yang Q, Shi W, Kahlert UD, Li Z, Lin S, Song Q, Fan W, Wang L, Zhu Y, Huang X. Mendelian Randomization Analyses of Chronic Immune-Mediated Diseases, Circulating Inflammatory Biomarkers, and Cytokines in Relation to Liver Cancer. Cancers (Basel) 2023; 15:cancers15112930. [PMID: 37296892 DOI: 10.3390/cancers15112930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Liver cancer is closely linked to chronic inflammation. While observational studies have reported positive associations between extrahepatic immune-mediated diseases and systemic inflammatory biomarkers and liver cancer, the genetic association between these inflammatory traits and liver cancer remains elusive and merits further investigation. We conducted a two-sample Mendelian randomization (MR) analysis, using inflammatory traits as exposures and liver cancer as the outcome. The genetic summary data of both exposures and outcome were retrieved from previous genome-wide association studies (GWAS). Four MR methods, including inverse-variance-weighted (IVW), MR-Egger regression, weighted-median, and weighted-mode methods, were employed to examine the genetic association between inflammatory traits and liver cancer. Nine extrahepatic immune-mediated diseases, seven circulating inflammatory biomarkers, and 187 inflammatory cytokines were analyzed in this study. The IVW method suggested that none of the nine immune-mediated diseases were associated with the risk of liver cancer, with odds ratios of 1.08 (95% CI 0.87-1.35) for asthma, 0.98 (95% CI 0.91-1.06) for rheumatoid arthritis, 1.01 (95% CI 0.96-1.07) for type 1 diabetes, 1.01 (95% CI 0.98-1.03) for psoriasis, 0.98 (95% CI 0.89-1.08) for Crohn's disease, 1.02 (95% CI 0.91-1.13) for ulcerative colitis, 0.91 (95% CI 0.74-1.11) for celiac disease, 0.93 (95% CI 0.84-1.05) for multiple sclerosis, and 1.05 (95% CI 0.97-1.13) for systemic lupus erythematosus. Similarly, no significant association was found between circulating inflammatory biomarkers and cytokines and liver cancer after correcting for multiple testing. The findings were consistent across all four MR methods used in this study. Our findings do not support a genetic association between extrahepatic inflammatory traits and liver cancer. However, larger-scale GWAS summary data and more genetic instruments are needed to confirm these findings.
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Affiliation(s)
- Qiushi Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570100, China
| | - Qiuxi Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570100, China
| | - Wenjie Shi
- Molecular and Experimental Surgery, University Clinic for General-, Visceral-, Vascular- and Trans-Plantation Surgery, Medical Faculty University Hospital Magdeburg, Otto-von Guericke University, 39120 Magdeburg, Germany
| | - Ulf D Kahlert
- Molecular and Experimental Surgery, University Clinic for General-, Visceral-, Vascular- and Trans-Plantation Surgery, Medical Faculty University Hospital Magdeburg, Otto-von Guericke University, 39120 Magdeburg, Germany
| | - Zhongyi Li
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Shibu Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570100, China
| | - Qifeng Song
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570100, China
| | - Weiqiang Fan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570100, China
| | - Li Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570100, China
| | - Yi Zhu
- Department of Gastroenterological Surgery, The Affiliated Hospital of Jiaxing University, Jiaxing 314001, China
| | - Xiaolong Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou 570100, China
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Li T, Feng Y, Wang C, Shi T, Abudurexiti A, Zhang M, Gao F. Assessment of causal associations among gut microbiota, metabolites, and celiac disease: a bidirectional Mendelian randomization study. Front Microbiol 2023; 14:1087622. [PMID: 37250054 PMCID: PMC10213403 DOI: 10.3389/fmicb.2023.1087622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Background A growing number of studies have implicated that gut microbial abundance and metabolite concentration alterations are associated with celiac disease (CD). However, the causal relationship underlying these associations is unclear. Here, we used Mendelian randomization (MR) to reveal the causal effect of gut microbiota and metabolites on CD. Methods Genome-wide association study (GWAS) summary-level data for gut microbiota, metabolites, and CD were extracted from published GWASs. Causal bacterial taxa and metabolites for CD were determined by two-sample MR analyses. The robustness of the results was assessed with sensitivity analyses. Finally, reverse causality was investigated with a reverse MR analysis. Results Genetically, increased genus Bifidobacterium was potentially associated with higher CD risk (odds ratio [OR] = 1.447, 95% confidence interval [CI]: 1.054-1.988, p = 0.022) while phylum Lentisphaerae (OR = 0.798, 95% CI: 0.648-0.983, p = 0.034) and genus Coprobacter (OR = 0.683, 95% CI: 0.531-0.880, p = 0.003) were related to lower CD risk. Moreover, there were suggestive associations between CD and the following seven metabolites: 1-oleoylglycerophosphoethanolamine, 1-palmitoylglycerophosphoethanolamine, 1,6-anhydroglucose, phenylacetylglutamine, tryptophan betaine, 10-undecenoate, and tyrosine. Sensitivity analyses deemed the results reliable without pleiotropy. Conclusion We investigated the causal relationships between gut microbiota, metabolites, and CD with two-sample MR. Our findings suggest several novel potential therapeutic targets for CD treatment. Further understanding of the underlying mechanism may provide insights into CD pathogenesis.
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Affiliation(s)
- Ting Li
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Yan Feng
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Chun Wang
- Department of Pathology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Tian Shi
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Adilai Abudurexiti
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Mengxia Zhang
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Feng Gao
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
- Xinjiang Clinical Research Center for Digestive Diseases, Urumqi, Xinjiang, China
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Pandey R, Bakay M, Hakonarson H. CLEC16A-An Emerging Master Regulator of Autoimmunity and Neurodegeneration. Int J Mol Sci 2023; 24:ijms24098224. [PMID: 37175930 PMCID: PMC10179542 DOI: 10.3390/ijms24098224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
CLEC16A is emerging as an important genetic risk factor for several autoimmune disorders and for Parkinson disease (PD), opening new avenues for translational research and therapeutic development. While the exact role of CLEC16A in health and disease is still being elucidated, the gene plays a critical role in the regulation of autophagy, mitophagy, endocytosis, intracellular trafficking, immune function, and in biological processes such as insulin secretion and others that are important to cellular homeostasis. As shown in both human and animal modeling studies, CLEC16A hypofunction predisposes to both autoinflammatory phenotype and neurodegeneration. While the two are clearly related, further functional studies are needed to fully understand the mechanisms involved for optimized therapeutic interventions. Based on recent data, mitophagy-inducing drugs may be warranted, and such therapy should be tested in clinical trials as these drugs would tackle the underlying pathogenic mechanism (s) and could treat or prevent symptoms of autoimmunity and neurodegeneration in individuals with CLEC16A risk variants. Accordingly, interventions directed at reversing the dysregulated mitophagy and the consequences of loss of function of CLEC16A without activating other detrimental cellular pathways could present an effective therapy. This review presents the emerging role of CLEC16A in health and disease and provides an update on the disease processes that are attributed to variants located in the CLEC16A gene, which are responsible for autoimmune disorders and neurodegeneration with emphasis on how this information is being translated into practical and effective applications in the clinic.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA 19104-4318, USA
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37
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Welander NZ, Rukh G, Rask-Andersen M, Harder AVE, van den Maagdenberg AMJM, Schiöth HB, Mwinyi J. Migraine, inflammatory bowel disease and celiac disease: A Mendelian randomization study. Headache 2023; 63:642-651. [PMID: 36705326 DOI: 10.1111/head.14470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 01/28/2023]
Abstract
OBJECTIVE To assess whether migraine may be genetically and/or causally associated with inflammatory bowel disease (IBD) or celiac disease. BACKGROUND Migraine has been linked to IBD and celiac disease in observational studies, but whether this link may be explained by a shared genetic basis or could be causal has not been established. The presence of a causal association could be clinically relevant, as treating one of these medical conditions might mitigate the symptoms of a causally linked condition. METHODS Linkage disequilibrium score regression and two-sample bidirectional Mendelian randomization analyses were performed using summary statistics from cohort-based genome-wide association studies of migraine (59,674 cases; 316,078 controls), IBD (25,042 cases; 34,915 controls) and celiac disease (11,812 or 4533 cases; 11,837 or 10,750 controls). Migraine with and without aura were analyzed separately, as were the two IBD subtypes Crohn's disease and ulcerative colitis. Positive control analyses and conventional Mendelian randomization sensitivity analyses were performed. RESULTS Migraine was not genetically correlated with IBD or celiac disease. No evidence was observed for IBD (odds ratio [OR] 1.00, 95% confidence interval [CI] 0.99-1.02, p = 0.703) or celiac disease (OR 1.00, 95% CI 0.99-1.02, p = 0.912) causing migraine or migraine causing either IBD (OR 1.08, 95% CI 0.96-1.22, p = 0.181) or celiac disease (OR 1.08, 95% CI 0.79-1.48, p = 0.614) when all participants with migraine were analyzed jointly. There was some indication of a causal association between celiac disease and migraine with aura (OR 1.04, 95% CI 1.00-1.08, p = 0.045), between celiac disease and migraine without aura (OR 0.95, 95% CI 0.92-0.99, p = 0.006), as well as between migraine without aura and ulcerative colitis (OR 1.15, 95% CI 1.02-1.29, p = 0.025). However, the results were not significant after multiple testing correction. CONCLUSIONS We found no evidence of a shared genetic basis or of a causal association between migraine and either IBD or celiac disease, although we obtained some indications of causal associations with migraine subtypes.
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Affiliation(s)
- Nike Zoe Welander
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Gull Rukh
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Aster V E Harder
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arn M J M van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jessica Mwinyi
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
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Martín-Masot R, Herrador-López M, Navas-López VM, Carmona FD, Nestares T, Bossini-Castillo L. Celiac Disease Is a Risk Factor for Mature T and NK Cell Lymphoma: A Mendelian Randomization Study. Int J Mol Sci 2023; 24:ijms24087216. [PMID: 37108375 PMCID: PMC10139431 DOI: 10.3390/ijms24087216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Celiac disease (CeD) is an immune-mediated disorder triggered by gluten ingestion that damages the small intestine. Although CeD has been associated with a higher risk for cancer, the role of CeD as a risk factor for specific malignancies, such as enteropathy-associated T-cell lymphoma (EATL), remains controversial. Using two-sample Mendelian randomization (2SMR) methods and the summarized results of large genome-wide association studies from public repositories, we addressed the causal relationship between CeD and eight different malignancies. Eleven non-HLA SNPs were selected as instrumental variables (IVs), and causality estimates were obtained using four 2SMR methods: random-effects inverse variance-weighted, weighted median estimation, MR-Egger regression, and MR pleiotropy residual sum and outlier (MR-PRESSO). We identified a significant causal relationship between CeD and mature T/NK cell lymphomas. Under a multivariate Mendelian randomization model, we observed that the causal effect of CeD was not dependent on other known lymphoma risk factors. We found that the most instrumental IV was located in the TAGAP locus, suggesting that aberrant T cell activation might be relevant in the T/NK cell malignization process. Our findings provide new insights into the connection between immune imbalance and the development of severe comorbidities, such as EATL, in patients with CeD.
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Affiliation(s)
- Rafael Martín-Masot
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
- Instituto de Nutrición y Tecnología de los Alimentos "José Mataix Verdú" (INYTA), Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
| | - Marta Herrador-López
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
| | - Víctor Manuel Navas-López
- Sección de Gastroenterología y Nutrición Infantil, Hospital Regional Universitario de Málaga, 29011 Málaga, Spain
| | - Francisco David Carmona
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Reproducción Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnologías Biomédicas, Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Teresa Nestares
- Instituto de Nutrición y Tecnología de los Alimentos "José Mataix Verdú" (INYTA), Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Departamento de Fisiología, Facultad de Farmacia, Universidad de Granada, 18071 Granada, Spain
| | - Lara Bossini-Castillo
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18016 Granada, Spain
- Reproducción Humana y Enfermedades Hereditarias y Complejas (IBS-TEC14), Terapias Avanzadas y Tecnologías Biomédicas, Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
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Chen J, Yuan S, Fu T, Ruan X, Qiao J, Wang X, Li X, Gill D, Burgess S, Giovannucci EL, Larsson SC. Gastrointestinal Consequences of Type 2 Diabetes Mellitus and Impaired Glycemic Homeostasis: A Mendelian Randomization Study. Diabetes Care 2023; 46:828-835. [PMID: 36800530 PMCID: PMC10091506 DOI: 10.2337/dc22-1385] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/17/2023] [Indexed: 02/19/2023]
Abstract
OBJECTIVE We conducted a Mendelian randomization (MR) study to examine the associations of type 2 diabetes and glycemic traits with gastrointestinal diseases (GDs). RESEARCH DESIGN AND METHODS Uncorrelated genetic variants associated with type 2 diabetes (n = 231), fasting insulin (n = 38), fasting glucose (n = 71), and hemoglobin A1c (n = 75) at the genome-wide significance were selected as instrument variables. Genetic associations with 23 common GDs were obtained from the FinnGen and UK Biobank studies and other large consortia. RESULTS Genetic liability to type 2 diabetes was associated with the risk of 12 GDs. Per 1-unit increase in the log-transformed odds ratio (OR) of type 2 diabetes, the OR was 1.06 (95% CI, 1.03-1.09) for gastroesophageal reflux disease, 1.12 (95% CI, 1.07-1.17) for gastric ulcer, 1.11 (95% CI, 1.03-1.20) for acute gastritis, 1.07 (95% CI, 1.01-1.13) for chronic gastritis, 1.08 (95% CI, 1.03-1.12) for irritable bowel syndrome, 1.04 (95% CI, 1.01-1.07) for diverticular disease, 1.08 (95% CI, 1.02-1.14) for acute pancreatitis, 1.09 (95% CI, 1.05-1.12) for cholelithiasis, 1.09 (95% CI, 1.05-1.13) for cholelithiasis with cholecystitis, 1.29 (95% CI, 1.17-1.43) for nonalcoholic fatty liver disease, 1.12 (95% CI, 1.03-1.21) for liver cirrhosis, and 0.93 (95% CI, 0.89-0.97) for ulcerative colitis. Genetically predicted higher levels of fasting insulin and glucose were associated with six and one GDs, respectively. CONCLUSIONS Associations were found between genetic liability to type 2 diabetes and an increased risk of a broad range of GDs, highlighting the importance of GD prevention in patients with type 2 diabetes.
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Affiliation(s)
- Jie Chen
- School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tian Fu
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xixian Ruan
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jie Qiao
- Department of Endocrinology and Metabolism, the Second Affiliated Hospital of ZheJiang University School of Medicine, Hangzhou, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xue Li
- School of Public Health and The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, U.K
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, U.K
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, U.K
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - Edward L. Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Susanna C. Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
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40
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Ma Q, Shams H, Didonna A, Baranzini SE, Cree BAC, Hauser SL, Henry RG, Oksenberg JR. Integration of epigenetic and genetic profiles identifies multiple sclerosis disease-critical cell types and genes. Commun Biol 2023; 6:342. [PMID: 36997638 PMCID: PMC10063586 DOI: 10.1038/s42003-023-04713-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/14/2023] [Indexed: 04/01/2023] Open
Abstract
Genome-wide association studies (GWAS) successfully identified multiple sclerosis (MS) susceptibility variants. Despite this notable progress, understanding the biological context of these associations remains challenging, due in part to the complexity of linking GWAS results to causative genes and cell types. Here, we aimed to address this gap by integrating GWAS data with single-cell and bulk chromatin accessibility data and histone modification profiles from immune and nervous systems. MS-GWAS associations are significantly enriched in regulatory regions of microglia and peripheral immune cell subtypes, especially B cells and monocytes. Cell-specific polygenic risk scores were developed to examine the cumulative impact of the susceptibility genes on MS risk and clinical phenotypes, showing significant associations with risk and brain white matter volume. The findings reveal enrichment of GWAS signals in B cell and monocyte/microglial cell-types, consistent with the known pathology and presumed targets of effective MS therapeutics.
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Affiliation(s)
- Qin Ma
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Hengameh Shams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Alessandro Didonna
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA
| | - Sergio E Baranzini
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Bruce A C Cree
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Roland G Henry
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jorge R Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA.
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Avalos D, Rey G, Ribeiro DM, Ramisch A, Dermitzakis ET, Delaneau O. Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity. Commun Biol 2023; 6:335. [PMID: 36977773 PMCID: PMC10050075 DOI: 10.1038/s42003-023-04688-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
Studying the interplay between genetic variation, epigenetic changes, and regulation of gene expression is crucial to understand the modification of cellular states in various conditions, including immune diseases. In this study, we characterize the cell-specificity in three key cells of the human immune system by building cis maps of regulatory regions with coordinated activity (CRDs) from ChIP-seq peaks and methylation data. We find that only 33% of CRD-gene associations are shared between cell types, revealing how similarly located regulatory regions provide cell-specific modulation of gene activity. We emphasize important biological mechanisms, as most of our associations are enriched in cell-specific transcription factor binding sites, blood-traits, and immune disease-associated loci. Notably, we show that CRD-QTLs aid in interpreting GWAS findings and help prioritize variants for testing functional hypotheses within human complex diseases. Additionally, we map trans CRD regulatory associations, and among 207 trans-eQTLs discovered, 46 overlap with the QTLGen Consortium meta-analysis in whole blood, showing that mapping functional regulatory units using population genomics allows discovering important mechanisms in the regulation of gene expression in immune cells. Finally, we constitute a comprehensive resource describing multi-omics changes to gain a greater understanding of cell-type specific regulatory mechanisms of immunity.
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Affiliation(s)
- Diana Avalos
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Rey
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Diogo M Ribeiro
- Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Anna Ramisch
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Olivier Delaneau
- Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland.
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
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42
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Messenger AG, Harries M, Macbeth AE, Chiu WS, Holmes S, Tziotzios C, de Lusignan S. Alopecia areata and risk of common infections: a population-based cohort study. Clin Exp Dermatol 2023; 48:332-338. [PMID: 36702574 DOI: 10.1093/ced/llac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 01/22/2023]
Abstract
BACKGROUND It is not known whether alopecia areata (AA) is associated with a greater or reduced risk for infection. AIM We undertook a population-based study exploring associations between AA and common infections. METHODS We extracted primary care records from the UK Oxford-Royal College of General Practitioners Research and Surveillance Centre database (trial registration: NCT04239521). The incidence of common and viral infection composite outcomes, and individual respiratory, gastrointestinal (GI), skin, urinary tract, genital and herpes infections, were compared in people with AA (AA group, n = 10 391) and a propensity-matched control group (n = 41 564). Adjusted hazard ratios (aHRs), controlling for sociodemographic and clinical covariates, and comorbidities were used to estimate the association between AA and each infection over 5 years. RESULTS The incidence (per 100 person-years) of common infections was slightly higher in the AA group [14.2, 95% confidence interval (CI) 13.8-14.6] than the control group (11.7, 95% CI 11.5-11.9). In adjusted analysis, positive associations were observed for composite outcomes (common infections aHR 1.13, 95% CI 1.09-1.17; viral infections aHR 1.11, 95% CI 1.07-1.16) and with respiratory tract, GI, skin and herpes simplex infections (aHR range 1.09-1.32). Excluding people in the control group without a recent consultation with their general practitioner showed no association between AA and infection (common infections aHR 1.01, 95% CI 0.98-1.05, viral infections aHR 0.99, 95% CI 0.95-1.03). CONCLUSIONS The association between AA and common infection may represent a higher propensity of people with AA to engage with healthcare services (and thereby to have infections recorded), rather than a true association between AA and infection. Overall our findings suggest that AA is not associated with a clinically significantly increased or decreased incidence of common infections.
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Affiliation(s)
| | - Matthew Harries
- The Dermatology Centre, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Salford, UK
- Centre for Dermatology Research, Manchester Academic Health Science Centre (MAHSC) & NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, UK
| | - Abby E Macbeth
- Department of Dermatology, Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Wing Sin Chiu
- Pfizer Ltd, Walton on the Hill, Tadworth, Surrey, UK
| | - Susan Holmes
- Alan Lyell Centre for Dermatology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Christos Tziotzios
- St John's Institute of Dermatology, King's College London, Guys Hospital, London, UK
| | - Simon de Lusignan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, UK
- Royal College of General Practitioners, Research and Surveillance Centre, London, UK
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43
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Khunsriraksakul C, Li Q, Markus H, Patrick MT, Sauteraud R, McGuire D, Wang X, Wang C, Wang L, Chen S, Shenoy G, Li B, Zhong X, Olsen NJ, Carrel L, Tsoi LC, Jiang B, Liu DJ. Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus. Nat Commun 2023; 14:668. [PMID: 36750564 PMCID: PMC9905560 DOI: 10.1038/s41467-023-36306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Systemic lupus erythematosus is a heritable autoimmune disease that predominantly affects young women. To improve our understanding of genetic etiology, we conduct multi-ancestry and multi-trait meta-analysis of genome-wide association studies, encompassing 12 systemic lupus erythematosus cohorts from 3 different ancestries and 10 genetically correlated autoimmune diseases, and identify 16 novel loci. We also perform transcriptome-wide association studies, computational drug repurposing analysis, and cell type enrichment analysis. We discover putative drug classes, including a histone deacetylase inhibitor that could be repurposed to treat lupus. We also identify multiple cell types enriched with putative target genes, such as non-classical monocytes and B cells, which may be targeted for future therapeutics. Using this newly assembled result, we further construct polygenic risk score models and demonstrate that integrating polygenic risk score with clinical lab biomarkers improves the diagnostic accuracy of systemic lupus erythematosus using the Vanderbilt BioVU and Michigan Genomics Initiative biobanks.
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Affiliation(s)
- Chachrit Khunsriraksakul
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Qinmengge Li
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Havell Markus
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Matthew T Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Renan Sauteraud
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Daniel McGuire
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Xingyan Wang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Chen Wang
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Lida Wang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Siyuan Chen
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ganesh Shenoy
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Nancy J Olsen
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Bibo Jiang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Dajiang J Liu
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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44
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Cui Y, Arnold FJ, Peng F, Wang D, Li JS, Michels S, Wagner EJ, La Spada AR, Li W. Alternative polyadenylation transcriptome-wide association study identifies APA-linked susceptibility genes in brain disorders. Nat Commun 2023; 14:583. [PMID: 36737438 PMCID: PMC9898543 DOI: 10.1038/s41467-023-36311-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Alternative polyadenylation (APA) plays an essential role in brain development; however, current transcriptome-wide association studies (TWAS) largely overlook APA in nominating susceptibility genes. Here, we performed a 3' untranslated region (3'UTR) APA TWAS (3'aTWAS) for 11 brain disorders by combining their genome-wide association studies data with 17,300 RNA-seq samples across 2,937 individuals. We identified 354 3'aTWAS-significant genes, including known APA-linked risk genes, such as SNCA in Parkinson's disease. Among these 354 genes, ~57% are not significant in traditional expression- and splicing-TWAS studies, since APA may regulate the translation, localization and protein-protein interaction of the target genes independent of mRNA level expression or splicing. Furthermore, we discovered ATXN3 as a 3'aTWAS-significant gene for amyotrophic lateral sclerosis, and its modulation substantially impacted pathological hallmarks of amyotrophic lateral sclerosis in vitro. Together, 3'aTWAS is a powerful strategy to nominate important APA-linked brain disorder susceptibility genes, most of which are largely overlooked by conventional expression and splicing analyses.
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Affiliation(s)
- Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
| | - Frederick J Arnold
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, School of Medicine, and the UCI Institute for Neurotherapeutics, University of California Irvine, Irvine, CA, 92697, USA
| | - Fanglue Peng
- Department of Molecular and Cellular Biology, University Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Wang
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA
| | - Sebastian Michels
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, School of Medicine, and the UCI Institute for Neurotherapeutics, University of California Irvine, Irvine, CA, 92697, USA
| | - Eric J Wagner
- School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, and Biological Chemistry, School of Medicine, and the UCI Institute for Neurotherapeutics, University of California Irvine, Irvine, CA, 92697, USA.
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, 92697, USA.
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45
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Zawistowski M, Fritsche LG, Pandit A, Vanderwerff B, Patil S, Schmidt EM, VandeHaar P, Willer CJ, Brummett CM, Kheterpal S, Zhou X, Boehnke M, Abecasis GR, Zöllner S. The Michigan Genomics Initiative: A biobank linking genotypes and electronic clinical records in Michigan Medicine patients. Cell Genom 2023; 3:100257. [PMID: 36819667 DOI: 10.1016/j.xgen.2023.100257] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/07/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
Biobanks of linked clinical patient histories and biological samples are an efficient strategy to generate large cohorts for modern genetics research. Biobank recruitment varies by factors such as geographic catchment and sampling strategy, which affect biobank demographics and research utility. Here, we describe the Michigan Genomics Initiative (MGI), a single-health-system biobank currently consisting of >91,000 participants recruited primarily during surgical encounters at Michigan Medicine. The surgical enrollment results in a biobank enriched for many diseases and ideally suited for a disease genetics cohort. Compared with the much larger population-based UK Biobank, MGI has higher prevalence for nearly all diagnosis-code-based phenotypes and larger absolute case counts for many phenotypes. Genome-wide association study (GWAS) results replicate known findings, thereby validating the genetic and clinical data. Our results illustrate that opportunistic biobank sampling within single health systems provides a unique and complementary resource for exploring the genetics of complex diseases.
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46
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Ivanova M, Bottiglieri L, Sajjadi E, Venetis K, Fusco N. Malignancies in Patients with Celiac Disease: Diagnostic Challenges and Molecular Advances. Genes (Basel) 2023; 14. [PMID: 36833303 DOI: 10.3390/genes14020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Celiac disease (CD) is a multiorgan autoimmune disorder of the chronic intestinal disease group characterized by duodenal inflammation in genetically predisposed individuals, precipitated by gluten ingestion. The pathogenesis of celiac disease is now widely studied, overcoming the limits of the purely autoimmune concept and explaining its hereditability. The genomic profiling of this condition has led to the discovery of numerous genes involved in interleukin signaling and immune-related pathways. The spectrum of disease manifestations is not limited to the gastrointestinal tract, and a significant number of studies have considered the possible association between CD and neoplasms. Patients with CD are found to be at increased risk of developing malignancies, with a particular predisposition of certain types of intestinal cancer, lymphomas, and oropharyngeal cancers. This can be partially explained by common cancer hallmarks present in these patients. The study of gut microbiota, microRNAs, and DNA methylation is evolving to find the any possible missing links between CD and cancer incidence in these patients. However, the literature is extremely mixed and, therefore, our understanding of the biological interplay between CD and cancer remains limited, with significant implications in terms of clinical management and screening protocols. In this review article, we seek to provide a comprehensive overview of the genomics, epigenomics, and transcriptomics data on CD and its relation to the most frequent types of neoplasms that may occur in these patients.
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Abstract
Among human leukocyte antigen (HLA)-associated disorders, celiac disease has an immunopathogenesis that is particularly well understood. The condition is characterized by hypersensitivity to cereal gluten proteins, and the disease lesion is localized in the gut. Still, the diagnosis can be made by detection of highly disease-specific autoantibodies to transglutaminase 2 in the blood. We now have mechanistic insights into how the disease-predisposing HLA-DQ molecules, via presentation of posttranslationally modified gluten peptides, are connected to the generation of these autoantibodies. This review presents our current understanding of the immunobiology of this common disorder that is positioned in the border zone between food hypersensitivity and autoimmunity.
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Affiliation(s)
- Rasmus Iversen
- KG Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; .,Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- KG Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; .,Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
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48
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Howarth S, Sneddon G, Allinson KR, Razvi S, Mitchell AL, Pearce SHS. Replication of association at the LPP and UBASH3A loci in a UK autoimmune Addison's disease cohort. Eur J Endocrinol 2023; 188:lvac010. [PMID: 36651163 DOI: 10.1093/ejendo/lvac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023]
Abstract
Autoimmune Addison's disease (AAD) arises from a complex interplay between multiple genetic susceptibility polymorphisms and environmental factors. The first genome wide association study (GWAS) with patients from Scandinavian Addison's registries has identified association signals at four novel loci in the genes LPP, SH2B3, SIGLEC5, and UBASH3A. To verify these novel risk loci, we performed a case-control association study in our independent cohort of 420 patients with AAD from the across the UK. We report significant association of alleles of the LPP and UBASH3A genes [odds ratio (95% confidence intervals), 1.46 (1.21-1.75)and 1.40 (1.16-1.68), respectively] with AAD in our UK cohort. In addition, we report nominal association of AAD with SH2B3 [OR 1.18 (1.02-1.35)]. We confirm that variants at the LPP and UBASH3A loci confer susceptibility to AAD in a UK population. Further studies with larger patient cohorts are required to robustly confirm the association of SH2B3 and SIGLEC5/SPACA6 alleles.
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Affiliation(s)
- Sophie Howarth
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Georgina Sneddon
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Kathleen R Allinson
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Salman Razvi
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Anna L Mitchell
- Department of Endocrinology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Simon H S Pearce
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Department of Endocrinology, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
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Yuan S, Kim JH, Xu P, Wang Z. Causal association between celiac disease and inflammatory bowel disease: A two-sample bidirectional Mendelian randomization study. Front Immunol 2023; 13:1057253. [PMID: 36685511 PMCID: PMC9845610 DOI: 10.3389/fimmu.2022.1057253] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Background An epidemiological link between celiac disease (CeD) and inflammatory bowel disease (IBD) has been well established recently. In this study, Mendelian randomization (MR) analysis was performed employing pooled data of publicly available genome-wide association studies (GWAS) to determine the causal relationship between CeD and IBD, encompassing ulcerative colitis (UC) and Crohn's disease (CD). Methods Dataset of CeD was acquired from GWAS for 12,041 cases and 12,228 controls. A GWAS of more than 86,000 patients and controls was used to identify genetic variations underlying IBD. MR analyses were performed with an inverse-variance-weighted approach, an MR-Egger regression, a weighted-mode approach, a weighted-median method, and sensitivity analyses of MR pleiotropy residual sum and outlie (MR-PRESSO). Results MR demonstrated that genetic predisposition to CeD was linked to a augmented risk of IBD (OR: 1.1408; 95% CI: 1.0614-1.2261; P = 0.0003). In the analysis of the two IBD subtypes, genetic predisposition to CeD was also linked to increased risks of UC (OR: 1.1646; 95% CI: 1.0614-1.2779; P = 0.0012) and CD (OR: 1.1865; 95% CI: 1.0948-1.2859; P = 3.07E-05). Reverse MR analysis results revealed that genetic susceptibility to IBD and CD was correlated with an augmented risk of CeD. However, there was no genetic correlation between UC and CeD. All of the above results were validated with other GWAS databases. Conclusion There is a bidirectional causal relationship of CeD with IBD and CD. However, UC only augments the risk of developing CeD.
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Affiliation(s)
- Shuai Yuan
- Division of Pancreatobiliary Surgery, Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Ji Hun Kim
- Division of Pancreatobiliary Surgery, Department of Surgery, Ajou University School of Medicine, Suwon, Republic of Korea,*Correspondence: Ji Hun Kim,
| | - Pai Xu
- Department of Orthopaedic Surgery, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Zhao Wang
- Department of Orthopaedic Surgery, Chungnam National University School of Medicine, Daejeon, Republic of Korea
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Noman M, Ahmed T, Ijaz U, Shahid M, Nazir MM, White JC, Li D, Song F. Bio-Functionalized Manganese Nanoparticles Suppress Fusarium Wilt in Watermelon (Citrullus lanatus L.) by Infection Disruption, Host Defense Response Potentiation, and Soil Microbial Community Modulation. Small 2023; 19:e2205687. [PMID: 36382544 DOI: 10.1002/smll.202205687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The use of nanofabricated materials is being explored for the potential in crop disease management. Chemically synthesized micronutrient nanoparticles (NPs) have been shown to reduce crop diseases; however, the potential of biogenic manganese NPs (bio-MnNPs) in disease control is unknown. Here, the potential and mechanism of bio-MnNPs in suppression of watermelon Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon) are reported. Bio-MnNPs are synthesized by cell-free cultural filtrate of a waterrmelon rhizosphere bacterial strain Bacillus megaterium NOM14, and are found spherical in shape with a size range of 27.0-65.7 nm. Application of bio-MnNPs at 100 µg mL-1 increases Mn content in watermelon roots/shoots and improves growth performance through enhancing multiple physiological processes, including antioxidative capacity. Bio-MnNPs at 100 µg mL-1 suppress Fusarium wilt through inhibiting colonization and invasive growth of Fon in watermelon roots/stems, and inhibit Fon vegetative growth, conidiation, conidial morphology, and cellular integrity. Bio-MnNPs potentiate watermelon systemic acquired resistance by triggering the salicylic acid signaling upon Fon infection, and reshape the soil microbial community by improving fungal diversity. These findings demonstrate that bio-MnNPs suppress watermelon Fusarium wilt by multiple ex planta and in planta mechanisms, and offer a promising nano-enabled strategy for the sustainable management of crop diseases.
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Affiliation(s)
- Muhammad Noman
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Usman Ijaz
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, 7250, Australia
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
| | - Muhammad Mudassir Nazir
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Dayong Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fengming Song
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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