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Chatterjee S, Leach ST, Lui K, Mishra A. Symbiotic symphony: Understanding host-microbiota dialogues in a spatial context. Semin Cell Dev Biol 2024; 161-162:22-30. [PMID: 38564842 DOI: 10.1016/j.semcdb.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Modern precision sequencing techniques have established humans as a holobiont that live in symbiosis with the microbiome. Microbes play an active role throughout the life of a human ranging from metabolism and immunity to disease tolerance. Hence, it is of utmost significance to study the eukaryotic host in conjunction with the microbial antigens to obtain a complete picture of the host-microbiome crosstalk. Previous attempts at profiling host-microbiome interactions have been either superficial or been attempted to catalogue eukaryotic transcriptomic profile and microbial communities in isolation. Additionally, the nature of such immune-microbial interactions is not random but spatially organised. Hence, for a holistic clinical understanding of the interplay between hosts and microbiota, it's imperative to concurrently analyze both microbial and host genetic information, ensuring the preservation of their spatial integrity. Capturing these interactions as a snapshot in time at their site of action has the potential to transform our understanding of how microbes impact human health. In examining early-life microbial impacts, the limited presence of communities compels analysis within reduced biomass frameworks. However, with the advent of spatial transcriptomics we can address this challenge and expand our horizons of understanding these interactions in detail. In the long run, simultaneous spatial profiling of host-microbiome dialogues can have enormous clinical implications especially in gaining mechanistic insights into the disease prognosis of localised infections and inflammation. This review addresses the lacunae in host-microbiome research and highlights the importance of profiling them together to map their interactions while preserving their spatial context.
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Affiliation(s)
- Soumi Chatterjee
- Telethon Kids Institute, Perth Children Hospital, Perth, Western Australia 6009, Australia; Curtin Medical School, Curtin University, Perth, Western Australia 6102, Australia
| | - Steven T Leach
- Discipline Paediatrics, School of Clinical Medicine, University of New South Wales, Sydney 2052, Australia
| | - Kei Lui
- Department of Newborn Care, Royal Hospital for Women and Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine, University of New South Wales, Sydney 2052, Australia
| | - Archita Mishra
- Telethon Kids Institute, Perth Children Hospital, Perth, Western Australia 6009, Australia; Curtin Medical School, Curtin University, Perth, Western Australia 6102, Australia.
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2
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Kong L, Cao Y, He Y, Zhang Y. Role and molecular mechanism of NOD2 in chronic non-communicable diseases. J Mol Med (Berl) 2024; 102:787-799. [PMID: 38740600 DOI: 10.1007/s00109-024-02451-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Nucleotide-binding oligomerization domain containing 2 (NOD2), located in the cell cytoplasm, is a pattern recognition receptor belonging to the innate immune receptor family. It mediates the innate immune response by identifying conserved sequences in bacterial peptide glycans and plays an essential role in maintaining immune system homeostasis. Gene mutations of NOD2 lead to the development of autoimmune diseases such as Crohn's disease and Blau syndrome. Recently, NOD2 has been shown to be associated with the pathogenesis of diabetes, cardiac-cerebral diseases, and cancers. However, the function of NOD2 in these non-communicable diseases (CNCDs) is not well summarized in reviews. Our report mainly discusses the primary function and molecular mechanism of NOD2 as well as its potential clinical significance in CNCDs.
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Affiliation(s)
- Lingjun Kong
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Weiqi Road, Huaiyin District, Jinan, Shandong, People's Republic of China
| | - Yanhua Cao
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Weiqi Road, Huaiyin District, Jinan, Shandong, People's Republic of China
| | - Yanan He
- Gamma Knife Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Yahui Zhang
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No. 324, Jingwu Weiqi Road, Huaiyin District, Jinan, Shandong, People's Republic of China.
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3
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Mizukami K, Dorsey-Oresto A, Raj K, Eringis A, Furrow E, Martin E, Yamanaka D, Kehl A, Kolicheski A, Jagannathan V, Leeb T, Lionakis MS, Giger U. Increased susceptibility to Mycobacterium avium complex infection in miniature Schnauzer dogs caused by a codon deletion in CARD9. Sci Rep 2024; 14:10346. [PMID: 38710903 PMCID: PMC11074286 DOI: 10.1038/s41598-024-61054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
Mammals are generally resistant to Mycobacterium avium complex (MAC) infections. We report here on a primary immunodeficiency disorder causing increased susceptibility to MAC infections in a canine breed. Adult Miniature Schnauzers developing progressive systemic MAC infections were related to a common founder, and pedigree analysis was consistent with an autosomal recessive trait. A genome-wide association study and homozygosity mapping using 8 infected, 9 non-infected relatives, and 160 control Miniature Schnauzers detected an associated region on chromosome 9. Whole genome sequencing of 2 MAC-infected dogs identified a codon deletion in the CARD9 gene (c.493_495del; p.Lys165del). Genotyping of Miniature Schnauzers revealed the presence of this mutant CARD9 allele worldwide, and all tested MAC-infected dogs were homozygous mutants. Peripheral blood mononuclear cells from a dog homozygous for the CARD9 variant exhibited a dysfunctional CARD9 protein with impaired TNF-α production upon stimulation with the fungal polysaccharide β-glucan that activates the CARD9-coupled C-type lectin receptor, Dectin-1. While CARD9-deficient knockout mice are susceptible to experimental challenges by fungi and mycobacteria, Miniature Schnauzer dogs with systemic MAC susceptibility represent the first spontaneous animal model of CARD9 deficiency, which will help to further elucidate host defense mechanisms against mycobacteria and fungi and assess potential therapies for animals and humans.
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Affiliation(s)
- Keijiro Mizukami
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genotyping Development, Yokohama, Kanagawa, Japan.
| | - Angella Dorsey-Oresto
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karthik Raj
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Eringis
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eva Furrow
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Errolyn Martin
- Wildlife Center of North Georgia, Inc., Acworth, GA, USA
| | - Daisuke Yamanaka
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | | | - Ana Kolicheski
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Urs Giger
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Vetsuisse Faculty, University of Zürich, Zurich, Switzerland.
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4
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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; 56:838-845. [PMID: 38741015 DOI: 10.1038/s41588-024-01732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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5
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Hou D, Yu T, Lu X, Hong JY, Yang M, Zi Y, Ho TT, Lin H. Sirt2 inhibition improves gut epithelial barrier integrity and protects mice from colitis. Proc Natl Acad Sci U S A 2024; 121:e2319833121. [PMID: 38648480 PMCID: PMC11066986 DOI: 10.1073/pnas.2319833121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/03/2024] [Indexed: 04/25/2024] Open
Abstract
Sirt2 is a nicotinamide adenine dinucleotide (NAD+)-dependent protein lysine deacylase that can remove both acetyl group and long-chain fatty acyl groups from lysine residues of many proteins. It was reported to affect inflammatory bowel disease (IBD) symptoms in a mouse model. However, conflicting roles were reported, with genetic knockout aggravating while pharmacological inhibition alleviating IBD symptoms. These seemingly conflicting reports cause confusion and deter further efforts in developing Sirt2 inhibitors as a potential treatment strategy for IBD. We investigated these conflicting reports and elucidated the role of Sirt2 in the mouse model of IBD. We essentially replicated these conflicting results and confirmed that Sirt2 inhibitors' protective effect is not through off-targets as two very different Sirt2 inhibitors (TM and AGK2) showed similar protection in the IBD mouse model. We believe that the differential effects of inhibitors and knockout are due to the fact that the Sirt2 inhibitors only inhibit some but not all the activities of Sirt2. This hypothesis is confirmed by the observation that a PROTAC degrader of Sirt2 did not protect mice in the IBD model, similar to Sirt2 knockout. Our study provides an interesting example where genetic knockout and pharmacological inhibition do not align and emphasizes the importance of developing substrate-dependent inhibitors. Importantly, we showed that the effect of Sirt2 inhibition in IBD is through regulating the gut epithelium barrier by inhibiting Arf6-mediated endocytosis of E-cadherin, a protein important for the intestinal epithelial integrity. This mechanistic understanding further supports Sirt2 as a promising therapeutic target for treating IBD.
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Affiliation(s)
- Dan Hou
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Tao Yu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- HHMI, Cornell University, Ithaca, NY14853
| | - Xuan Lu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Jun Young Hong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Min Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Yanlin Zi
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Thanh Tu Ho
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- HHMI, Cornell University, Ithaca, NY14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
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6
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Marafini I, Monteleone I, Laudisi F, Monteleone G. Aryl Hydrocarbon Receptor Signalling in the Control of Gut Inflammation. Int J Mol Sci 2024; 25:4527. [PMID: 38674118 PMCID: PMC11050475 DOI: 10.3390/ijms25084527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Aryl hydrocarbon receptor (AHR), a transcription factor activated by many natural and synthetic ligands, represents an important mediator of the interplay between the environment and the host's immune responses. In a healthy gut, AHR activation promotes tolerogenic signals, which help maintain mucosal homeostasis. AHR expression is defective in the inflamed gut of patients with inflammatory bowel diseases (IBD), where decreased AHR signaling is supposed to contribute to amplifying the gut tissue's destructive immune-inflammatory responses. We here review the evidence supporting the role of AHR in controlling the "physiological" intestinal inflammation and summarize the data about the therapeutic effects of AHR activators, both in preclinical mouse models of colitis and in patients with IBD.
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Affiliation(s)
- Irene Marafini
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, 00133 Rome, Italy;
| | - Ivan Monteleone
- Department of Biomedicine and Prevention, University of “Tor Vergata”, 00133 Rome, Italy;
| | - Federica Laudisi
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy;
| | - Giovanni Monteleone
- Gastroenterology Unit, Policlinico Universitario Tor Vergata, 00133 Rome, Italy;
- Department of Systems Medicine, University of “Tor Vergata”, 00133 Rome, Italy;
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7
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Kayali S, Fantasia S, Gaiani F, Cavallaro LG, de'Angelis GL, Laghi L. NOD2 and Crohn's Disease Clinical Practice: From Epidemiology to Diagnosis and Therapy, Rewired. Inflamm Bowel Dis 2024:izae075. [PMID: 38582044 DOI: 10.1093/ibd/izae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Indexed: 04/08/2024]
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease with a multifactorial pathogenesis involving environmental and genetic factors. Since the late 20th century, the discovery of the first susceptibility gene (NOD2, previously referred to as CARD15) for CD has paved the way for further investigations into the correlations between clinical features and genetics, and its potential impact on clinical practice has fueled the research in the last 2 decades. Recent therapeutic advancements involving novel biologic drugs and small molecules have shifted inflammatory bowel disease management from a disease-centered to a patient-centric approach. To date, the role of NOD2 has not been fully understood yet. Recent data suggest that its clinical impact may be greater than currently recognized. This review overviews the most common NOD2 variants' role in real-life clinical practice. These genetic variants increase the risk of developing the disease and can aid in tailoring diagnosis and treatment. They are associated with the stricturing phenotype and ileal involvement and increase the risk of steroid refractoriness. In the meantime, limited and inconclusive evidence exists regarding their predictive role in response to azathioprine, biologic drugs, and small molecules. Eventually, their role in increasing the risk for surgery is evident, especially in those with the L1007fs variant. If further trials will support the initial evidence reported so far, NOD2 genetic variants will emerge as possible candidates for developing precision medicine in CD.
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Affiliation(s)
- Stefano Kayali
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Stefano Fantasia
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Federica Gaiani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Gastroenterology and Endoscopy Unit, University Hospital of Parma, Parma, Italy
| | | | | | - Luigi Laghi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Laboratory of Molecular Gastroenterology, Humanitas Clinical and Research Centre, Rozzano, Italy
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8
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Xiao L, Qi L, Fu R, Nie Q, Zhang X, Luo W. A large-scale comparison of the meat quality characteristics of different chicken breeds in South China. Poult Sci 2024; 103:103740. [PMID: 38701629 PMCID: PMC11087722 DOI: 10.1016/j.psj.2024.103740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
Meat quality traits are essential for producing high-quality broilers, but the genetic improvement has been limited by the complexity of measurement methods and the numerous traits involved. To systematically understand the meat quality characteristics of different broiler breeds, this study collected data on slaughter performance, skin color, fat deposition, and meat quality traits of 434 broilers from 12 different breeds in South China. The results showed that there was no significant difference in the live weight and slaughter weight of various broiler breeds at their respective market ages. Commercial broiler breeds such as Xiaobai and Huangma chickens had higher breast muscle and leg muscle rates. The skin and abdominal fat of Huangma chickens cultivated in the consumer market in South China exhibited significantly higher levels of yellowness compared to other varieties. Concerning fat traits, we observed that Wenchang chickens exhibited a strong ability to fat deposition, while the younger breeds showed lower fat deposition. Additionally, there were significant positive correlations found among different traits, including traits related to weight, traits related to fat, and skin color of different parts. Hierarchical clustering analysis revealed that fast-growing and large broiler Xiaobai chickens formed a distinct cluster based on carcass characteristics, skin color, and meat quality traits. Principal component analysis (PCA) was used to extract multiple principal components as substitutes for complex meat quality indicators, establishing a chicken meat quality evaluation model to differentiate between different breeds of chickens. At the same time, we identified 46, 22, and 20 SNP loci and their adjacent genes that were significantly associated with muscle mass traits, fat deposition, and skin color through genome-wide association studies (GWAS). The above results are helpful for systematically understanding the differences and characteristics of meat quality traits among different breeds.
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Affiliation(s)
- Liangchao Xiao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Lin Qi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Rong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
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9
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Alfayyadh MM, Maksemous N, Sutherland HG, Lea RA, Griffiths LR. Unravelling the Genetic Landscape of Hemiplegic Migraine: Exploring Innovative Strategies and Emerging Approaches. Genes (Basel) 2024; 15:443. [PMID: 38674378 PMCID: PMC11049430 DOI: 10.3390/genes15040443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Migraine is a severe, debilitating neurovascular disorder. Hemiplegic migraine (HM) is a rare and debilitating neurological condition with a strong genetic basis. Sequencing technologies have improved the diagnosis and our understanding of the molecular pathophysiology of HM. Linkage analysis and sequencing studies in HM families have identified pathogenic variants in ion channels and related genes, including CACNA1A, ATP1A2, and SCN1A, that cause HM. However, approximately 75% of HM patients are negative for these mutations, indicating there are other genes involved in disease causation. In this review, we explored our current understanding of the genetics of HM. The evidence presented herein summarises the current knowledge of the genetics of HM, which can be expanded further to explain the remaining heritability of this debilitating condition. Innovative bioinformatics and computational strategies to cover the entire genetic spectrum of HM are also discussed in this review.
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Affiliation(s)
| | | | | | | | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia; (M.M.A.); (N.M.); (H.G.S.); (R.A.L.)
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10
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Brandt M, Cao Z, Krishna C, Reedy JL, Gu X, Dutko RA, Oliver BA, Tusi BK, Park J, Richey L, Segerstolpe Å, Litwiler S, Creasey EA, Carey KL, Vyas JM, Graham DB, Xavier RJ. Translational genetics identifies a phosphorylation switch in CARD9 required for innate inflammatory responses. Cell Rep 2024; 43:113944. [PMID: 38489265 PMCID: PMC11008285 DOI: 10.1016/j.celrep.2024.113944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/07/2024] [Accepted: 02/24/2024] [Indexed: 03/17/2024] Open
Abstract
Population genetics continues to identify genetic variants associated with diseases of the immune system and offers a unique opportunity to discover mechanisms of immune regulation. Multiple genetic variants linked to severe fungal infections and autoimmunity are associated with caspase recruitment domain-containing protein 9 (CARD9). We leverage the CARD9 R101C missense variant to uncover a biochemical mechanism of CARD9 activation essential for antifungal responses. We demonstrate that R101C disrupts a critical signaling switch whereby phosphorylation of S104 releases CARD9 from an autoinhibited state to promote inflammatory responses in myeloid cells. Furthermore, we show that CARD9 R101C exerts dynamic effects on the skin cellular contexture during fungal infection, corrupting inflammatory signaling and cell-cell communication circuits. Card9 R101C mice fail to control dermatophyte infection in the skin, resulting in high fungal burden, yet show minimal signs of inflammation. Together, we demonstrate how translational genetics reveals molecular and cellular mechanisms of innate immune regulation.
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Affiliation(s)
- Marta Brandt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zhifang Cao
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Chirag Krishna
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jennifer L Reedy
- Division of Infectious Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xiebin Gu
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Richard A Dutko
- Division of Infectious Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Blayne A Oliver
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Betsabeh Khoramian Tusi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jihye Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lauren Richey
- Tufts Comparative Medicine Services, Tufts University, Boston, MA 02111, USA
| | - Åsa Segerstolpe
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott Litwiler
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Elizabeth A Creasey
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Jatin M Vyas
- Division of Infectious Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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11
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Wang J, Sun M, Liu X, Yan Q, Gao Q, Ni K, Yang J, Zhang S, Zhang C, Shan C. Transcriptome analysis identifies genetic risk markers and explores the pathogenesis for inflammatory bowel disease. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167013. [PMID: 38199515 DOI: 10.1016/j.bbadis.2023.167013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
Inflammatory bowel disease (IBD) is an incurable and disabling bowel disease driven by multiple risk factors that severely limit patients' quality of life. We integrated the RNA-sequencing data of 1238 IBD patients, and investigated the pathogenesis of IBD by combining transcriptional element prediction analysis and immune-related analysis. Here, we first determined that KIAA1109 is inhibited in IBD patients. The expression of KIAA1109 and NOD2, the key receptor of NOD-like receptors, showed a negative correlation. The NOD-like receptor signaling pathway is activated and exerts transcriptional regulation on the chemokines CXCL1 and CXCL2 through the activation of the transcription factors NFκB and AP1. Analysis of immune infiltration revealed that the expression of chemokines CXCL1 and CXCL2 may regulate the inflammatory response induced by immune cells. These findings suggest that the KIAA1109-NOD2-NFκB/AP1-CXCL1/CXCL2 regulatory axis is the molecular mechanism of IBD pathogenesis, which will provide a new perspective for the diagnosis, treatment and management of IBD patients.
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Affiliation(s)
- Jiyan Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Mingming Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Xu Liu
- Endoscopy Center, Tianjin Union Medical Center, Tianjin 300121, China
| | - Qi Yan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Qingle Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Kemin Ni
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China
| | - Juze Yang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Shuai Zhang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Chunze Zhang
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin 300121, China; Tianjin Institute of Coloproctology, Tianjin 300121, China.
| | - Changliang Shan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China.
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12
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Staal J, Driege Y, Van Gaever F, Steels J, Beyaert R. Chimeric and mutant CARD9 constructs enable analyses of conserved and diverged autoinhibition mechanisms in the CARD-CC protein family. FEBS J 2024; 291:1220-1245. [PMID: 38098267 DOI: 10.1111/febs.17035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/09/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Caspase recruitment domain-containing protein (CARD)9, CARD10, CARD11, and CARD14 all belong to the CARD-coiled coil (CC) protein family and originated from a single common ancestral protein early in vertebrate evolution. All four proteins form CARD-CC/BCL10/MALT1 (CBM) complexes leading to nuclear factor-kappa-B (NF-κB) activation after upstream phosphorylation by various protein kinase C (PKC) isoforms. CBM complex signaling is critical for innate and adaptive immunity, but aberrant activation can cause autoimmune or autoinflammatory diseases, or be oncogenic. CARD9 shows a superior auto-inhibition compared with other CARD-CC family proteins, with very low spontaneous activity when overexpressed in HEK293T cells. In contrast, the poor auto-inhibition of other CARD-CC family proteins, especially CARD10 (CARMA3) and CARD14 (CARMA2), is hampering characterization of upstream activators or activating mutations in overexpression studies. We grafted different domains from CARD10, 11, and 14 on CARD9 to generate chimeric CARD9 backbones for functional characterization of activating mutants using NF-κB reporter gene activation in HEK293T cells as readout. CARD11 (CARMA1) activity was not further reduced by grafting on CARD9 backbones. The chimeric CARD9 approach was subsequently validated by using several known disease-associated mutations in CARD10 and CARD14, and additional screening allowed us to identify several previously unknown activating natural variants in human CARD9 and CARD10. Using Genebass as a resource of exome-based disease association statistics, we found that activated alleles of CARD9 correlate with irritable bowel syndrome (IBS), constipation, osteoarthritis, fibromyalgia, insomnia, anxiety, and depression, which can occur as comorbidities.
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Affiliation(s)
- Jens Staal
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Yasmine Driege
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Femke Van Gaever
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Jill Steels
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
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13
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Zhang P, Zhang W, Sun W, Xu J, Hu H, Wang L, Wong L. Identification of gene biomarkers for brain diseases via multi-network topological semantics extraction and graph convolutional network. BMC Genomics 2024; 25:175. [PMID: 38350848 PMCID: PMC10865627 DOI: 10.1186/s12864-024-09967-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Brain diseases pose a significant threat to human health, and various network-based methods have been proposed for identifying gene biomarkers associated with these diseases. However, the brain is a complex system, and extracting topological semantics from different brain networks is necessary yet challenging to identify pathogenic genes for brain diseases. RESULTS In this study, we present a multi-network representation learning framework called M-GBBD for the identification of gene biomarker in brain diseases. Specifically, we collected multi-omics data to construct eleven networks from different perspectives. M-GBBD extracts the spatial distributions of features from these networks and iteratively optimizes them using Kullback-Leibler divergence to fuse the networks into a common semantic space that represents the gene network for the brain. Subsequently, a graph consisting of both gene and large-scale disease proximity networks learns representations through graph convolution techniques and predicts whether a gene is associated which brain diseases while providing associated scores. Experimental results demonstrate that M-GBBD outperforms several baseline methods. Furthermore, our analysis supported by bioinformatics revealed CAMP as a significantly associated gene with Alzheimer's disease identified by M-GBBD. CONCLUSION Collectively, M-GBBD provides valuable insights into identifying gene biomarkers for brain diseases and serves as a promising framework for brain networks representation learning.
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Affiliation(s)
- Ping Zhang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weihan Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hubei Hongshan Laboratory, Wuhan, 430074, China
| | - Weicheng Sun
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Xu
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Hu
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China.
| | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China.
- Guangxi Key Lab of Human-Machine Interaction and Intelligent Decision, Guangxi Academy of Sciences, Nanning, 530007, China.
| | - Leon Wong
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, 518118, China.
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14
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Zaki MB, Abulsoud AI, Ashraf A, Abdelmaksoud NM, Sallam AAM, Aly SH, Sa'eed El-Tokhy F, Rashad AA, El-Dakroury WA, Abdel Mageed SS, Nomier Y, Elrebehy MA, Elshaer SS, Elballal MS, Mohammed OA, Abdel-Reheim MA, Doghish AS. The potential role of miRNAs in the pathogenesis of schizophrenia - A focus on signaling pathways interplay. Pathol Res Pract 2024; 254:155102. [PMID: 38211386 DOI: 10.1016/j.prp.2024.155102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
microRNAs (miRNAs) play a crucial role in brain growth and function. Hence, research on miRNA has the potential to reveal much about the etiology of neuropsychiatric diseases. Among these, schizophrenia (SZ) is a highly intricate and destructive neuropsychiatric ailment that has been thoroughly researched in the field of miRNA. Despite being a relatively recent area of study about miRNAs and SZ, this discipline has advanced enough to justify numerous reviews that summarize the findings from the past to the present. However, most reviews cannot cover all research, thus it is necessary to synthesize the large range of publications on this topic systematically and understandably. Consequently, this review aimed to provide evidence that miRNAs play a role in the pathophysiology and progression of SZ. They have also been investigated for their potential use as biomarkers and therapeutic targets.
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Affiliation(s)
- Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Menoufia 32897, Egypt
| | - Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Alaa Ashraf
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | | | - Al-Aliaa M Sallam
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Shaza H Aly
- Department of Pharmacognosy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Fatma Sa'eed El-Tokhy
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed A Rashad
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Walaa A El-Dakroury
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Yousra Nomier
- Department of Pharmacology and Clinical Pharmacy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Shereen Saeid Elshaer
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Department of Biochemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11823, Egypt
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia.
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef 62521, Egypt.
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
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15
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Hadebe MT, Malgwi SA, Okpeku M. Revolutionizing Malaria Vector Control: The Importance of Accurate Species Identification through Enhanced Molecular Capacity. Microorganisms 2023; 12:82. [PMID: 38257909 PMCID: PMC10818655 DOI: 10.3390/microorganisms12010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Many factors, such as the resistance to pesticides and a lack of knowledge of the morphology and molecular structure of malaria vectors, have made it more challenging to eradicate malaria in numerous malaria-endemic areas of the globe. The primary goal of this review is to discuss malaria vector control methods and the significance of identifying species in vector control initiatives. This was accomplished by reviewing methods of molecular identification of malaria vectors and genetic marker classification in relation to their use for species identification. Due to its specificity and consistency, molecular identification is preferred over morphological identification of malaria vectors. Enhanced molecular capacity for species identification will improve mosquito characterization, leading to accurate control strategies/treatment targeting specific mosquito species, and thus will contribute to malaria eradication. It is crucial for disease epidemiology and surveillance to accurately identify the Plasmodium spp. that are causing malaria in patients. The capacity for disease surveillance will be significantly increased by the development of more accurate, precise, automated, and high-throughput diagnostic techniques. In conclusion, although morphological identification is quick and achievable at a reduced cost, molecular identification is preferred for specificity and sensitivity. To achieve the targeted malaria elimination goal, proper identification of vectors using accurate techniques for effective control measures should be prioritized.
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Affiliation(s)
| | | | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
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16
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Lötstedt B, Stražar M, Xavier R, Regev A, Vickovic S. Spatial host-microbiome sequencing reveals niches in the mouse gut. Nat Biotechnol 2023:10.1038/s41587-023-01988-1. [PMID: 37985876 DOI: 10.1038/s41587-023-01988-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/12/2023] [Indexed: 11/22/2023]
Abstract
Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host-microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host-bacteria interactions. SHM-seq should enhance the study of native host-microbe interactions in health and disease.
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Affiliation(s)
- Britta Lötstedt
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- New York Genome Center, New York, NY, USA
| | | | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts, General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
| | - Sanja Vickovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- New York Genome Center, New York, NY, USA.
- Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA.
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden.
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17
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Carlson SL, Mathew L, Savage M, Kok K, Lindsay JO, Munro CA, McCarthy NE. Mucosal Immunity to Gut Fungi in Health and Inflammatory Bowel Disease. J Fungi (Basel) 2023; 9:1105. [PMID: 37998910 PMCID: PMC10672531 DOI: 10.3390/jof9111105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
The gut microbiome is a diverse microbial community composed of bacteria, viruses, and fungi that plays a major role in human health and disease. Dysregulation of these gut organisms in a genetically susceptible host is fundamental to the pathogenesis of inflammatory bowel disease (IBD). While bacterial dysbiosis has been a predominant focus of research for many years, there is growing recognition that fungal interactions with the host immune system are an important driver of gut inflammation. Candida albicans is likely the most studied fungus in the context of IBD, being a near universal gut commensal in humans and also a major barrier-invasive pathogen. There is emerging evidence that intra-strain variation in C. albicans virulence factors exerts a critical influence on IBD pathophysiology. In this review, we describe the immunological impacts of variations in C. lbicans colonisation, morphology, genetics, and proteomics in IBD, as well as the clinical and therapeutic implications.
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Affiliation(s)
- Sean L. Carlson
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
- Gastroenterology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Liya Mathew
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Michael Savage
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Klaartje Kok
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
- Gastroenterology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - James O. Lindsay
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
- Gastroenterology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Carol A. Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Neil E. McCarthy
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
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18
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Stafford IS, Ashton JJ, Mossotto E, Cheng G, Mark Beattie R, Ennis S. Supervised Machine Learning Classifies Inflammatory Bowel Disease Patients by Subtype Using Whole Exome Sequencing Data. J Crohns Colitis 2023; 17:1672-1680. [PMID: 37205778 PMCID: PMC10637043 DOI: 10.1093/ecco-jcc/jjad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Inflammatory bowel disease [IBD] is a chronic inflammatory disorder with two main subtypes: Crohn's disease [CD] and ulcerative colitis [UC]. Prompt subtype diagnosis enables the correct treatment to be administered. Using genomic data, we aimed to assess machine learning [ML] to classify patients according to IBD subtype. METHODS Whole exome sequencing [WES] from paediatric/adult IBD patients was processed using an in-house bioinformatics pipeline. These data were condensed into the per-gene, per-individual genomic burden score, GenePy. Data were split into training and testing datasets [80/20]. Feature selection with a linear support vector classifier, and hyperparameter tuning with Bayesian Optimisation, were performed [training data]. The supervised ML method random forest was utilised to classify patients as CD or UC, using three panels: 1] all available genes; 2] autoimmune genes; 3] 'IBD' genes. ML results were assessed using area under the receiver operating characteristics curve [AUROC], sensitivity, and specificity on the testing dataset. RESULTS A total of 906 patients were included in analysis [600 CD, 306 UC]. Training data included 488 patients, balanced according to the minority class of UC. The autoimmune gene panel generated the best performing ML model [AUROC = 0.68], outperforming an IBD gene panel [AUROC = 0.61]. NOD2 was the top gene for discriminating CD and UC, regardless of the gene panel used. Lack of variation in genes with high GenePy scores in CD patients was the best classifier of a diagnosis of UC. DISCUSSION We demonstrate promising classification of patients by subtype using random forest and WES data. Focusing on specific subgroups of patients, with larger datasets, may result in better classification.
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Affiliation(s)
- Imogen S Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Enrico Mossotto
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Guo Cheng
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research, University Hospital Southampton, Southampton, UK
| | - Robert Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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19
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Acencio ML, Ostaszewski M, Mazein A, Rosenstiel P, Aden K, Mishra N, Andersen V, Sidiropoulos P, Banos A, Filia A, Rahmouni S, Finckh A, Gu W, Schneider R, Satagopam V. The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease. Front Immunol 2023; 14:1257321. [PMID: 38022524 PMCID: PMC10646502 DOI: 10.3389/fimmu.2023.1257321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Chronic inflammatory diseases (CIDs), including inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are thought to emerge from an impaired complex network of inter- and intracellular biochemical interactions among several proteins and small chemical compounds under strong influence of genetic and environmental factors. CIDs are characterised by shared and disease-specific processes, which is reflected by partially overlapping genetic risk maps and pathogenic cells (e.g., T cells). Their pathogenesis involves a plethora of intracellular pathways. The translation of the research findings on CIDs molecular mechanisms into effective treatments is challenging and may explain the low remission rates despite modern targeted therapies. Modelling CID-related causal interactions as networks allows us to tackle the complexity at a systems level and improve our understanding of the interplay of key pathways. Here we report the construction, description, and initial applications of the SYSCID map (https://syscid.elixir-luxembourg.org/), a mechanistic causal interaction network covering the molecular crosstalk between IBD, RA and SLE. We demonstrate that the map serves as an interactive, graphical review of IBD, RA and SLE molecular mechanisms, and helps to understand the complexity of omics data. Examples of such application are illustrated using transcriptome data from time-series gene expression profiles following anti-TNF treatment and data from genome-wide associations studies that enable us to suggest potential effects to altered pathways and propose possible mechanistic biomarkers of treatment response.
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Affiliation(s)
- Marcio Luis Acencio
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- ELIXIR Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Vibeke Andersen
- Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University Hospital of Southern Denmark, Aabenraa, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Prodromos Sidiropoulos
- Rheumatology and Clinical Immunology, Medical School, University of Crete, Heraklion, Greece
- Laboratory of Rheumatology, Autoimmunity and Inflammation, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology (IMBB-FORTH), Heraklion, Greece
| | - Aggelos Banos
- Autoimmunity and Inflammation Laboratory, Biomedical Research Foundation of the Academy of Athens, Athens and Laboratory of Molecular Hematology, Democritus University of Thrace, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Anastasia Filia
- Autoimmunity and Inflammation Laboratory, Biomedical Research Foundation of the Academy of Athens, Athens and Laboratory of Molecular Hematology, Democritus University of Thrace, University Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Souad Rahmouni
- Unit of Animal Genomics, GIGA-Institute, University of Liège, Liège, Belgium
| | - Axel Finckh
- Rheumatology Division, Geneva University Hospital (HUG), Geneva, Switzerland
- Geneva Center for Inflammation Research (GCIR), University of Geneva (UNIGE), Geneva, Switzerland
| | - Wei Gu
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- ELIXIR Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- ELIXIR Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- ELIXIR Luxembourg, Esch-sur-Alzette, Luxembourg
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20
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Kitashova A, Brodsky V, Chaturvedi P, Pierides I, Ghatak A, Weckwerth W, Nägele T. Quantifying the impact of dynamic plant-environment interactions on metabolic regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 290:154116. [PMID: 37839392 DOI: 10.1016/j.jplph.2023.154116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.
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Affiliation(s)
- Anastasia Kitashova
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Vladimir Brodsky
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Palak Chaturvedi
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Iro Pierides
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Arindam Ghatak
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Wolfram Weckwerth
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
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21
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Hou JJ, Ma AH, Qin YH. Activation of the aryl hydrocarbon receptor in inflammatory bowel disease: insights from gut microbiota. Front Cell Infect Microbiol 2023; 13:1279172. [PMID: 37942478 PMCID: PMC10628454 DOI: 10.3389/fcimb.2023.1279172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory intestinal disease that affects more than 3.5 million people, with rising prevalence. It deeply affects patients' daily life, increasing the burden on patients, families, and society. Presently, the etiology of IBD remains incompletely clarified, while emerging evidence has demonstrated that altered gut microbiota and decreased aryl hydrocarbon receptor (AHR) activity are closely associated with IBD. Furthermore, microbial metabolites are capable of AHR activation as AHR ligands, while the AHR, in turn, affects the microbiota through various pathways. In light of the complex connection among gut microbiota, the AHR, and IBD, it is urgent to review the latest research progress in this field. In this review, we describe the role of gut microbiota and AHR activation in IBD and discussed the crosstalk between gut microbiota and the AHR in the context of IBD. Taken as a whole, we propose new therapeutic strategies targeting the AHR-microbiota axis for IBD, even for other related diseases caused by AHR-microbiota dysbiosis.
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Affiliation(s)
| | | | - Yue-Hua Qin
- Department of Gastroenterology, Shaoxing People’s Hospital, Shaoxing, China
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22
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Roberts MD, McCarthy JJ, Hornberger TA, Phillips SM, Mackey AL, Nader GA, Boppart MD, Kavazis AN, Reidy PT, Ogasawara R, Libardi CA, Ugrinowitsch C, Booth FW, Esser KA. Mechanisms of mechanical overload-induced skeletal muscle hypertrophy: current understanding and future directions. Physiol Rev 2023; 103:2679-2757. [PMID: 37382939 PMCID: PMC10625844 DOI: 10.1152/physrev.00039.2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
Mechanisms underlying mechanical overload-induced skeletal muscle hypertrophy have been extensively researched since the landmark report by Morpurgo (1897) of "work-induced hypertrophy" in dogs that were treadmill trained. Much of the preclinical rodent and human resistance training research to date supports that involved mechanisms include enhanced mammalian/mechanistic target of rapamycin complex 1 (mTORC1) signaling, an expansion in translational capacity through ribosome biogenesis, increased satellite cell abundance and myonuclear accretion, and postexercise elevations in muscle protein synthesis rates. However, several lines of past and emerging evidence suggest that additional mechanisms that feed into or are independent of these processes are also involved. This review first provides a historical account of how mechanistic research into skeletal muscle hypertrophy has progressed. A comprehensive list of mechanisms associated with skeletal muscle hypertrophy is then outlined, and areas of disagreement involving these mechanisms are presented. Finally, future research directions involving many of the discussed mechanisms are proposed.
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Affiliation(s)
- Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - John J McCarthy
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, United States
| | - Troy A Hornberger
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - Stuart M Phillips
- Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Abigail L Mackey
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Copenhagen University Hospital-Bispebjerg and Frederiksberg, and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Gustavo A Nader
- Department of Kinesiology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States
| | - Marni D Boppart
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
| | - Andreas N Kavazis
- School of Kinesiology, Auburn University, Auburn, Alabama, United States
| | - Paul T Reidy
- Department of Kinesiology, Nutrition and Health, Miami University, Oxford, Ohio, United States
| | - Riki Ogasawara
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Cleiton A Libardi
- MUSCULAB-Laboratory of Neuromuscular Adaptations to Resistance Training, Department of Physical Education, Federal University of São Carlos, São Carlos, Brazil
| | - Carlos Ugrinowitsch
- School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil
| | - Frank W Booth
- Department of Biomedical Sciences, University of Missouri, Columbia, Missouri, United States
| | - Karyn A Esser
- Department of Physiology and Aging, College of Medicine, University of Florida, Gainesville, Florida, United States
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23
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Ahangari M, Gentry AE, Hassan MF, Nguyen TH, Kendler KS, Bacanu SA, Peterson RE, Riley BP, Webb BT. Improving the discovery of rare variants associated with alcohol problems by leveraging machine learning phenotype prediction and functional information. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557163. [PMID: 37745400 PMCID: PMC10515858 DOI: 10.1101/2023.09.11.557163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Alcohol use disorder (AUD) is moderately heritable with significant social and economic impact. Genome-wide association studies (GWAS) have identified common variants associated with AUD, however, rare variant investigations have yet to achieve well-powered sample sizes. In this study, we conducted an interval-based exome-wide analysis of the Alcohol Use Disorder Identification Test Problems subscale (AUDIT-P) using both machine learning (ML) predicted risk and empirical functional weights. This research has been conducted using the UK Biobank Resource (application number 30782.) Filtering the 200k exome release to unrelated individuals of European ancestry resulted in a sample of 147,386 individuals with 51,357 observed and 96,029 unmeasured but predicted AUDIT-P for exome analysis. Sequence Kernel Association Test (SKAT/SKAT-O) was used for rare variant (Minor Allele Frequency (MAF) < 0.01) interval analyses using default and empirical weights. Empirical weights were constructed using annotations found significant by stratified LD Score Regression analysis of predicted AUDIT-P GWAS, providing prior functional weights specific to AUDIT-P. Using only samples with observed AUDIT-P yielded no significantly associated intervals. In contrast, ADH1C and THRA gene intervals were significant (False discovery rate (FDR) <0.05) using default and empirical weights in the predicted AUDIT-P sample, with the most significant association found using predicted AUDIT-P and empirical weights in the ADH1C gene (SKAT-O P Default = 1.06 x 10 -9 and P Empirical weight = 6.25 x 10 -11 ). These findings provide evidence for rare variant association of the ADH1C gene with the AUDIT-P and highlight the successful leveraging of ML to increase effective sample size and prior empirical functional weights based on common variant GWAS data to refine and increase the statistical significance in underpowered phenotypes.
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24
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Batista-Liz JC, Calvo-Río V, Sebastián Mora-Gil M, Sevilla-Pérez B, Márquez A, Leonardo MT, Peñalba A, Carmona FD, Narvaez J, Martín-Penagos L, Belmar-Vega L, Gómez-Fernández C, Caminal-Montero L, Collado P, Quiroga-Colina P, Uriarte-Ecenarro M, Rubio E, Luque ML, Blanco-Madrigal JM, Galíndez-Agirregoikoa E, Martín J, Castañeda S, González-Gay MA, Blanco R, Pulito-Cueto V, López-Mejías R. Mucosal Immune Defence Gene Polymorphisms as Relevant Players in the Pathogenesis of IgA Vasculitis? Int J Mol Sci 2023; 24:13063. [PMID: 37685869 PMCID: PMC10488110 DOI: 10.3390/ijms241713063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
ITGAM-ITGAX (rs11150612, rs11574637), VAV3 rs17019602, CARD9 rs4077515, DEFA (rs2738048, rs10086568), and HORMAD2 rs2412971 are mucosal immune defence polymorphisms, that have an impact on IgA production, described as risk loci for IgA nephropathy (IgAN). Since IgAN and Immunoglobulin-A vasculitis (IgAV) share molecular mechanisms, with the aberrant deposit of IgA1 being the main pathophysiologic feature of both entities, we assessed the potential influence of the seven abovementioned polymorphisms on IgAV pathogenesis. These seven variants were genotyped in 381 Caucasian IgAV patients and 997 matched healthy controls. No statistically significant differences were observed in the genotype and allele frequencies of these seven polymorphisms when the whole cohort of IgAV patients and those with nephritis were compared to controls. Similar genotype and allele frequencies of all polymorphisms were disclosed when IgAV patients were stratified according to the age at disease onset or the presence/absence of gastrointestinal or renal manifestations. Likewise, no ITGAM-ITGAX and DEFA haplotype differences were observed when the whole cohort of IgAV patients, along with those with nephritis and controls, as well as IgAV patients, stratified according to the abovementioned clinical characteristics, were compared. Our results suggest that mucosal immune defence polymorphisms do not represent novel genetic risk factors for IgAV pathogenesis.
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Affiliation(s)
- Joao Carlos Batista-Liz
- Immunopathology Group, Rheumatology Department, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (J.C.B.-L.); (V.C.-R.); (M.S.M.-G.); (R.B.)
| | - Vanesa Calvo-Río
- Immunopathology Group, Rheumatology Department, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (J.C.B.-L.); (V.C.-R.); (M.S.M.-G.); (R.B.)
| | - María Sebastián Mora-Gil
- Immunopathology Group, Rheumatology Department, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (J.C.B.-L.); (V.C.-R.); (M.S.M.-G.); (R.B.)
| | - Belén Sevilla-Pérez
- Division of Paediatrics, Hospital Universitario San Cecilio, 18016 Granada, Spain;
| | - Ana Márquez
- Instituto de Parasitología y Biomedicina ‘López-Neyra’, CSIC, PTS Granada, 18016 Granada, Spain; (A.M.); (J.M.)
| | - María Teresa Leonardo
- Division of Paediatrics, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain; (M.T.L.); (A.P.)
| | - Ana Peñalba
- Division of Paediatrics, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain; (M.T.L.); (A.P.)
| | - Francisco David Carmona
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, 18071 Granada, Spain;
- Instituto de Investigación Biosanitaria ibs. Granada, 18012 Granada, Spain
| | - Javier Narvaez
- Division of Rheumatology, Hospital Universitario de Bellvitge, 08907 Barcelona, Spain;
| | - Luis Martín-Penagos
- Immunopathology Group, Division of Nephrology, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (L.M.-P.); (L.B.-V.)
| | - Lara Belmar-Vega
- Immunopathology Group, Division of Nephrology, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (L.M.-P.); (L.B.-V.)
| | | | - Luis Caminal-Montero
- Internal Medicine Department, Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain;
| | - Paz Collado
- Division of Rheumatology, Hospital Universitario Severo Ochoa, 28911 Madrid, Spain;
| | - Patricia Quiroga-Colina
- Division of Rheumatology, Hospital Universitario de La Princesa, IIS-Princesa, 28006 Madrid, Spain; (P.Q.-C.); (M.U.-E.); (S.C.)
| | - Miren Uriarte-Ecenarro
- Division of Rheumatology, Hospital Universitario de La Princesa, IIS-Princesa, 28006 Madrid, Spain; (P.Q.-C.); (M.U.-E.); (S.C.)
| | - Esteban Rubio
- Department of Rheumatology, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain; (E.R.); (M.L.L.)
| | - Manuel León Luque
- Department of Rheumatology, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain; (E.R.); (M.L.L.)
| | - Juan María Blanco-Madrigal
- Division of Rheumatology, Hospital Universitario de Basurto, 48013 Bilbao, Spain; (J.M.B.-M.); (E.G.-A.)
| | - Eva Galíndez-Agirregoikoa
- Division of Rheumatology, Hospital Universitario de Basurto, 48013 Bilbao, Spain; (J.M.B.-M.); (E.G.-A.)
| | - Javier Martín
- Instituto de Parasitología y Biomedicina ‘López-Neyra’, CSIC, PTS Granada, 18016 Granada, Spain; (A.M.); (J.M.)
| | - Santos Castañeda
- Division of Rheumatology, Hospital Universitario de La Princesa, IIS-Princesa, 28006 Madrid, Spain; (P.Q.-C.); (M.U.-E.); (S.C.)
| | - Miguel Angel González-Gay
- Department of Rheumatology, IIS-Fundación Jiménez Díaz, 28040 Madrid, Spain;
- School of Medicine, Universidad de Cantabria, 39011 Santander, Spain
| | - Ricardo Blanco
- Immunopathology Group, Rheumatology Department, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (J.C.B.-L.); (V.C.-R.); (M.S.M.-G.); (R.B.)
| | - Verónica Pulito-Cueto
- Immunopathology Group, Rheumatology Department, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (J.C.B.-L.); (V.C.-R.); (M.S.M.-G.); (R.B.)
| | - Raquel López-Mejías
- Immunopathology Group, Rheumatology Department, Hospital Universitario Marqués de Valdecilla-IDIVAL, 39011 Santander, Spain; (J.C.B.-L.); (V.C.-R.); (M.S.M.-G.); (R.B.)
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25
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Renauer P, Park JJ, Bai M, Acosta A, Lee WH, Lin GH, Zhang Y, Dai X, Wang G, Errami Y, Wu T, Clark P, Ye L, Yang Q, Chen S. Immunogenetic Metabolomics Reveals Key Enzymes That Modulate CAR T-cell Metabolism and Function. Cancer Immunol Res 2023; 11:1068-1084. [PMID: 37253111 PMCID: PMC10527769 DOI: 10.1158/2326-6066.cir-22-0565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/26/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
Immune evasion is a critical step of cancer progression that remains a major obstacle for current T cell-based immunotherapies. Hence, we investigated whether it is possible to genetically reprogram T cells to exploit a common tumor-intrinsic evasion mechanism whereby cancer cells suppress T-cell function by generating a metabolically unfavorable tumor microenvironment (TME). In an in silico screen, we identified ADA and PDK1 as metabolic regulators. We then showed that overexpression (OE) of these genes enhanced the cytolysis of CD19-specific chimeric antigen receptor (CAR) T cells against cognate leukemia cells, and conversely, ADA or PDK1 deficiency dampened this effect. ADA-OE in CAR T cells improved cancer cytolysis under high concentrations of adenosine, the ADA substrate, and an immunosuppressive metabolite in the TME. High-throughput transcriptomics and metabolomics analysis of these CAR T cells revealed alterations of global gene expression and metabolic signatures in both ADA- and PDK1-engineered CAR T cells. Functional and immunologic analyses demonstrated that ADA-OE increased proliferation and decreased exhaustion in CD19-specific and HER2-specific CAR T cells. ADA-OE improved tumor infiltration and clearance by HER2-specific CAR T cells in an in vivo colorectal cancer model. Collectively, these data unveil systematic knowledge of metabolic reprogramming directly in CAR T cells and reveal potential targets for improving CAR T-cell therapy.
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Affiliation(s)
- Paul Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
| | - Jonathan J. Park
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
- M.D.-Ph.D. Program, Yale University, West Haven, Connecticut, USA
| | - Meizhu Bai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Arianny Acosta
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Won-Ho Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Guang Han Lin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Yale College, Yale University, New Haven, Connecticut, USA
| | - Yueqi Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Guangchuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Youssef Errami
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Tulane University, New Orleans, LA, USA
| | - Terence Wu
- West Campus Analytical Core, Mass Spectrometry/Proteomics Facility, West Haven, Connecticut, USA
| | - Paul Clark
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
| | - Lupeng Ye
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Nanjing University, Nanjing, Jiangsu, China
| | - Quanjun Yang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Present Address: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
- Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
- M.D.-Ph.D. Program, Yale University, West Haven, Connecticut, USA
- Immunobiology Program, Yale University, New Haven, Connecticut, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut, USA
- Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Liver Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Wu-Tsai Center, Yale University, New Haven, Connecticut, USA
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26
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Kathrani A, Theelen B, Bond R. Isolation of Malassezia yeasts from dogs with gastrointestinal disease undergoing duodenal endoscopy. J Small Anim Pract 2023. [PMID: 37681754 DOI: 10.1111/jsap.13649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/03/2023] [Accepted: 06/08/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVES To culture Malassezia and other fungi from the duodenum of dogs with gastrointestinal signs undergoing routine endoscopic examination. MATERIALS AND METHODS Quantitative microbial culture was performed on duodenal juice aspirated from dogs with suspected enteropathy during routine upper gastrointestinal endoscopy; samples were cultured on Sabouraud's dextrose agar (30, 32 and 37°C) and modified Dixon agar (32°C) for 14 days. Isolates were identified phenotypically and by matrix-assisted laser desorption ionisation-time of flight, and internal transcribed spacer sequencing. Yeast presence was also evaluated by cytological and histopathological examination of smears and biopsy specimens. RESULTS Forty-five dogs were recruited with chronic inflammatory enteropathy (n=38), granulomatous colitis (n=2), gastric adenocarcinoma (n=2), duodenal small cell lymphoma (n=1) and idiopathic severe gastrointestinal haemorrhage (n=2). Fungi were cultured from 14 dogs: Malassezia pachydermatis was isolated from eight [chronic inflammatory enteropathy (n=7) (along with Candida albicans n=1); granulomatous colitis (n=1)] and Malassezia sympodialis from another (gastric adenocarcinoma). Five dogs with chronic inflammatory enteropathy yielded other yeasts (C. albicans, Candida glabrata, Kazachstania slooffiae, Kazachstania telluris, Pichia kudriavzevii [syn. C. krusei]). Yeasts were never observed in histopathological specimens. Fluorescent microscopical examination of cytological specimens showed yeast in only one case, from which K. slooffiae was subsequently isolated. CLINICAL SIGNIFICANCE Based on a literature search, this is the first report of isolation of M. pachydermatis, M. sympodialis, K. slooffiae and K. telluris from the canine duodenum. Further studies are needed to determine whether these are resident or transient fungi in the canine duodenum and whether their presence has a pathogenic effect on the host.
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Affiliation(s)
- A Kathrani
- Clinical Science and Services, Royal Veterinary College, North Mymms, Hatfield, AL9 7TA, UK
| | - B Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - R Bond
- Clinical Science and Services, Royal Veterinary College, North Mymms, Hatfield, AL9 7TA, UK
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27
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Andersen V, Bennike TB, Bang C, Rioux JD, Hébert-Milette I, Sato T, Hansen AK, Nielsen OH. Investigating the Crime Scene-Molecular Signatures in Inflammatory Bowel Disease. Int J Mol Sci 2023; 24:11217. [PMID: 37446397 DOI: 10.3390/ijms241311217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are without cure and troublesome to manage because of the considerable diversity between patients and the lack of reliable biomarkers. Several studies have demonstrated that diet, gut microbiota, genetics and other patient factors are essential for disease occurrence and progression. Understanding the link between these factors is crucial for identifying molecular signatures that identify biomarkers to advance the management of IBD. Recent technological breakthroughs and data integration have fuelled the intensity of this research. This research demonstrates that the effect of diet depends on patient factors and gut microbial activity. It also identifies a range of potential biomarkers for IBD management, including mucosa-derived cytokines, gasdermins and neutrophil extracellular traps, all of which need further evaluation before clinical translation. This review provides an update on cutting-edge research in IBD that aims to improve disease management and patient quality of life.
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Affiliation(s)
- Vibeke Andersen
- Molecular Diagnostic and Clinical Research Unit, University Hospital of Southern Denmark, Institute of Regional Research, University of Southern Denmark, 5000 Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Tue B Bennike
- Molecular Diagnostic and Clinical Research Unit, University Hospital of Southern Denmark, Institute of Regional Research, University of Southern Denmark, 5000 Odense, Denmark
- Medical Microbiology and Immunology, Department of Health Science and Technology, Aalborg University, 9000 Aalborg, Denmark
| | - Corinna Bang
- Institute for Clinical Molecular Biology, Christian-Albrecht's University, 24105 Kiel, Germany
| | - John D Rioux
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
- Montreal Heart Institute Research Institute, Montreal, QC H1T 1C8, Canada
| | - Isabelle Hébert-Milette
- Department of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
- Montreal Heart Institute Research Institute, Montreal, QC H1T 1C8, Canada
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Axel K Hansen
- Experimental Animal Models, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Ole H Nielsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
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28
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Chen C, Yan W, Tao M, Fu Y. NAD + Metabolism and Immune Regulation: New Approaches to Inflammatory Bowel Disease Therapies. Antioxidants (Basel) 2023; 12:1230. [PMID: 37371959 DOI: 10.3390/antiox12061230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), is a multifactorial systemic inflammatory immune response. Nicotinamide adenine dinucleotide (NAD+) is a co-enzyme involved in cell signaling and energy metabolism. Calcium homeostasis, gene transcription, DNA repair, and cell communication involve NAD+ and its degradation products. There is a growing recognition of the intricate relationship between inflammatory diseases and NAD+ metabolism. In the case of IBD, the maintenance of intestinal homeostasis relies on a delicate balance between NAD+ biosynthesis and consumption. Consequently, therapeutics designed to target the NAD+ pathway are promising for the management of IBD. This review discusses the metabolic and immunoregulatory processes of NAD+ in IBD to examine the molecular biology and pathophysiology of the immune regulation of IBD and to provide evidence and theoretical support for the clinical use of NAD+ in IBD.
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Affiliation(s)
- Chaoyue Chen
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wei Yan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Meihui Tao
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yu Fu
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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29
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Liu Z, Liu R, Gao H, Jung S, Gao X, Sun R, Liu X, Kim Y, Lee HS, Kawai Y, Nagasaki M, Umeno J, Tokunaga K, Kinouchi Y, Masamune A, Shi W, Shen C, Guo Z, Yuan K, Zhu S, Li D, Liu J, Ge T, Cho J, Daly MJ, McGovern DPB, Ye BD, Song K, Kakuta Y, Li M, Huang H. Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries. Nat Genet 2023; 55:796-806. [PMID: 37156999 PMCID: PMC10290755 DOI: 10.1038/s41588-023-01384-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/27/2023] [Indexed: 05/10/2023]
Abstract
Inflammatory bowel diseases (IBDs) are chronic disorders of the gastrointestinal tract with the following two subtypes: Crohn's disease (CD) and ulcerative colitis (UC). To date, most IBD genetic associations were derived from individuals of European (EUR) ancestries. Here we report the largest IBD study of individuals of East Asian (EAS) ancestries, including 14,393 cases and 15,456 controls. We found 80 IBD loci in EAS alone and 320 when meta-analyzed with ~370,000 EUR individuals (~30,000 cases), among which 81 are new. EAS-enriched coding variants implicate many new IBD genes, including ADAP1 and GIT2. Although IBD genetic effects are generally consistent across ancestries, genetics underlying CD appears more ancestry dependent than UC, driven by allele frequency (NOD2) and effect (TNFSF15). We extended the IBD polygenic risk score (PRS) by incorporating both ancestries, greatly improving its accuracy and highlighting the importance of diversity for the equitable deployment of PRS.
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Affiliation(s)
- Zhanju Liu
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Ruize Liu
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Han Gao
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Xiang Gao
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruicong Sun
- Center for IBD Research, Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoming Liu
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yongjae Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshitaka Kinouchi
- Student Healthcare Center, Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Wenzhao Shi
- Digital Health China Technologies Corp Ltd., Beijing, China
| | - Chengguo Shen
- Digital Health China Technologies Corp Ltd., Beijing, China
| | - Zhenglin Guo
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kai Yuan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shu Zhu
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Dalin Li
- Widjaja Inflammatory Bowel Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tian Ge
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dermot P B McGovern
- Widjaja Inflammatory Bowel Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Byong Duk Ye
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea.
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Mingsong Li
- Inflammatory Bowel Diseases Research Center, Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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30
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Al-Jawabreh A, Ereqat S, Al-Jawabreh H, Dumaidi K, Nasereddin A. Genetic diversity and haplotype analysis of Leishmania tropica identified in sand fly vectors of the genera Phlebotomus and Sergentomyia using next-generation sequencing technology. Parasitol Res 2023; 122:1351-1360. [PMID: 37036520 DOI: 10.1007/s00436-023-07835-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023]
Abstract
Next-generation sequencing (NGS) was used to investigate the genetic diversity of Leishmania tropica in the sand fly vector, targeting the internal transcribed spacer 1 (ITS1) of the genus Leishmania. Bioinformatics analyses were conducted using Galaxy, MEGA version X, DnaSP ver. 6.12.03, and PopART 1.7 software for NGS analysis, phylogenetic tree, genetic diversity, and haplotype networking, respectively. A total of 307 engorged sand flies were trapped, with an overall Leishmania infection rate of 9.4 (29/307) and 6.8% by NGS and ITS1-PCR, respectively. Two Leishmania-infected sand fly genera were identified: Phlebotomus (10.2%, 26/254) and Sergentomyia (5.7% (3/53). The phylogenetic tree showed two clusters, cluster I included the four study sequences along with 25 GenBank-retrieved DNA sequences. Cluster II consisted of three sequences from Iran and Pakistan. The genetic diversity analysis for the 29 L. tropica sequences showed high haplotype (gene) diversity index (Hd) (0.62 ± 0.07) but low nucleotide diversity index (π) (0.04 ± 0.01). Tajima's D, a neutrality test, is more negative in cluster I (D = - 2.0) than in total population (D = - 1.83), but both are equally significant (P < 0.001), indicating that observed variation in cluster I and whole population is less frequent than expected. The median-joining haplotype network produced a total of 11 active haplotypes. In conclusion, L. tropica from sand flies in Palestine is monophyletic that assembled in one main phylogroup and one haplotype.
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Affiliation(s)
- Amer Al-Jawabreh
- Arab American University, Jenin, Palestine
- Leishmaniases Research Unit-Jericho, Jericho, Palestine
| | - Suheir Ereqat
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Deis, East Jerusalem, Palestine.
| | - Hanan Al-Jawabreh
- Leishmaniases Research Unit-Jericho, Jericho, Palestine
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Deis, East Jerusalem, Palestine
| | | | - Abedelmajeed Nasereddin
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Deis, East Jerusalem, Palestine
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31
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Whole Exome Sequencing of Hemiplegic Migraine Patients Shows an Increased Burden of Missense Variants in CACNA1H and CACNA1I Genes. Mol Neurobiol 2023; 60:3034-3043. [PMID: 36786913 PMCID: PMC10122627 DOI: 10.1007/s12035-023-03255-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Hemiplegic migraine (HM) is a rare subtype of migraine with aura. Given that causal missense mutations in the voltage-gated calcium channel α1A subunit gene CACNA1A have been identified in a subset of HM patients, we investigated whether HM patients without a mutation have an increased burden of such variants in the "CACNA1x gene family". Whole exome sequencing data of an Australian cohort of unrelated HM patients (n = 184), along with public data from gnomAD, as controls, was used to assess the burden of missense variants in CACNA1x genes. We performed both a variant and a subject burden test. We found a significant burden for the number of variants in CACNA1E (p = 1.3 × 10-4), CACNA1H (p < 2.2 × 10-16) and CACNA1I (p < 2.2 × 10-16). There was also a significant burden of subjects with missense variants in CACNA1E (p = 6.2 × 10-3), CACNA1H (p < 2.2 × 10-16) and CACNA1I (p < 2.2 × 10-16). Both the number of variants and number of subjects were replicated for CACNA1H (p = 3.5 × 10-8; p = 0.012) and CACNA1I (p = 0.019, p = 0.044), respectively, in a Dutch clinical HM cohort (n = 32), albeit that CACNA1I did not remain significant after multiple testing correction. Our data suggest that HM, in the absence of a single causal mutation, is a complex trait, in which an increased burden of missense variants in CACNA1H and CACNA1I may contribute to the risk of disease.
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32
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Zhou C, Cai S, Xie Y, Zeng Z, Zhang J, Su G, Wu Q, Ye X, Cao Q, Yang P, Hu J. Genetic association of PRKCD and CARD9 polymorphisms with Vogt-Koyanagi-Harada disease in the Chinese Han population. Hum Genomics 2023; 17:9. [PMID: 36782298 PMCID: PMC9926551 DOI: 10.1186/s40246-023-00459-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Protein kinase C delta (PRKCD) and caspase recruitment domain family member 9 (CARD9) are genes involved in B and T cell activation, and cytokine production, which are vital mechanisms underlying autoimmune disease development. This study aimed to explore the association of the PRKCD and CARD9 genes with Vogt-Koyanagi-Harada disease (VKH) disease. The case-control study was performed to in 912 patients with VKH and 878 normal controls. MassARRAY system, SHEsis online platform, real-time PCR, and enzyme-linked immunosorbent assay were used to detect genotyping, haplotyping, mRNA expression, and cytokine levels, respectively. RESULTS We found that rs74437127 C allele of PRKCD, rs3812555 CC genotype, and C allele of CARD9 were associated with increased susceptibility of VKH (Pc = 0.020, OR = 1.624; Pc = 2.04 × 10-5, OR = 1.810; Pc = 2.76 × 10-5, OR = 1.698, respectively). However, the rs74437127 T allele, and rs3812555 TC genotype and T allele were linked with decreased susceptibility to VKH (Pc = 0.020, OR = 0.616; Pc = 7.85 × 10-5, OR = 0.559; Pc = 2.76 × 10-5, OR = 0.589, respectively). PRKCD ATG and CARD9 GCTTA haplotypes decreased susceptibility to VKH (Pc = 3.11 × 10-3, OR = 0.594; Pc = 5.00 × 10-3, OR = 0.639, respectively). Functional studies on rs3812555 genotyped individuals revealed that CC carriers had significantly higher CARD9 mRNA expression and tumour necrosis factor-α production than TC/TT carriers (P = 1.00 × 10-4; P = 2.00 × 10-3, respectively). CONCLUSIONS We found an association between PRKCD rs74437127 and CARD9 rs3812555 polymorphisms and VKH susceptibility and revealed that the increased susceptibility of rs3812555 for VKH may be mediated by regulating CARD9 gene expression and the production of pro-inflammatory cytokines, such as TNF-α.
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Affiliation(s)
- Chunya Zhou
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Shiya Cai
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Yuhong Xie
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Zhen Zeng
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Jun Zhang
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Guannan Su
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Qiuying Wu
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Xingsheng Ye
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Qingfeng Cao
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016, China.
| | - Jianmin Hu
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000, People's Republic of China. .,Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004, People's Republic of China.
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Jans D, Cleynen I. The genetics of non-monogenic IBD. Hum Genet 2023; 142:669-682. [PMID: 36720734 DOI: 10.1007/s00439-023-02521-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/10/2023] [Indexed: 02/02/2023]
Abstract
Inflammatory bowel disease (IBD), with Crohn's disease and ulcerative colitis as main subtypes, is a prototypical multifactorial disease with both genetic and environmental factors involved. Genetically, IBD covers a wide spectrum from monogenic to polygenic forms. In polygenic disease, many genetic variants each contribute a small amount to disease risk. With the advent of genome-wide association studies (GWAS), it became possible to find these variants and corresponding genes, leading so far to the discovery of ca 240 loci associated with IBD. Together, these however explain only 20-25% of the heritability of IBD, leaving a large portion unaccounted for. This missing heritability might be hidden in common variants with even lower effect than the ones currently found through GWAS, but also in rare variants which can be found through large-scale sequencing studies or potentially in multiplex families. In this review, we will give an overview of the current knowledge about the genetics of non-monogenic IBD and how it differs from the monogenic form(s), and future perspectives. The history of IBD genetic studies from twin studies over linkage studies to GWAS, and finally large-scale sequencing studies and the revisiting of multiplex families will be discussed.
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Affiliation(s)
- Deborah Jans
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Herestraat 49, box610, 3000, Louvain, Belgium
| | - Isabelle Cleynen
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Herestraat 49, box610, 3000, Louvain, Belgium.
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34
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Mahmoudi H, Hossainpour H. Application and development of fecal microbiota transplantation in the treatment of gastrointestinal and metabolic diseases: A review. Saudi J Gastroenterol 2023; 29:3-11. [PMID: 36412458 PMCID: PMC10117003 DOI: 10.4103/sjg.sjg_131_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Fecal microbiota transplantation (FMT) restores a balanced intestinal flora, which helps to cure recurrent Clostridium difficile infections (RCDI). FMT has also been used to treat other gastrointestinal diseases, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and chronic constipation, as well as a variety of non-GI disorders. The purpose of this review is to discuss gut microbiota and FMT treatment of GI and non-GI diseases. An imbalanced gut microbiota is known to predispose one to Clostridium difficile infections (CDI), IBD, and IBS. However, the complex role of the gut microbiota in maintaining health is a newer concept that is being increasingly studied. The microbiome plays a major role in cellular immunity and metabolism and has been implicated in the pathogenesis of non-GI autoimmune diseases, chronic fatigue syndrome, obesity, and even some neuropsychiatric disorders. Many recent studies have reported that viral gastroenteritis can affect intestinal epithelial cells, and SARS-CoV-2 virus has been identified in the stool of infected patients. FMT is a highly effective cure for RCDI, but a better understanding of the gut microbiota in maintaining health and controlled studies of FMT in a variety of conditions are needed before FMT can be accepted and used clinically.
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Affiliation(s)
- Hassan Mahmoudi
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences; Department of Nursing and Paramedical, Nahavand School of Allied Medical Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hadi Hossainpour
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Saadh MJ, Mikhailova MV, Rasoolzadegan S, Falaki M, Akhavanfar R, Gonzáles JLA, Rigi A, Kiasari BA. Therapeutic potential of mesenchymal stem/stromal cells (MSCs)-based cell therapy for inflammatory bowel diseases (IBD) therapy. Eur J Med Res 2023; 28:47. [PMID: 36707899 PMCID: PMC9881387 DOI: 10.1186/s40001-023-01008-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/10/2023] [Indexed: 01/28/2023] Open
Abstract
Recently, mesenchymal stem/stromal cells (MSCs) therapy has become an emerging therapeutic modality for the treatment of inflammatory bowel disease (IBD), given their immunoregulatory and pro-survival attributes. MSCs alleviate dysregulated inflammatory responses through the secretion of a myriad of anti-inflammatory mediators, such as interleukin 10 (IL-10), transforming growth factor-β (TGFβ), prostaglandin E2 (PGE2), tumor necrosis factor-stimulated gene-6 (TSG-6), etc. Indeed, MSC treatment of IBD is largely carried out through local microcirculation construction, colonization and repair, and immunomodulation, thus alleviating diseases severity. The clinical therapeutic efficacy relies on to the marked secretion of various secretory molecules from viable MSCs via paracrine mechanisms that are required for gut immuno-microbiota regulation and the proliferation and differentiation of surrounding cells like intestinal epithelial cells (IECs) and intestinal stem cells (ISCs). For example, MSCs can induce IECs proliferation and upregulate the expression of tight junction (TJs)-associated protein, ensuring intestinal barrier integrity. Concerning the encouraging results derived from animal studies, various clinical trials are conducted or ongoing to address the safety and efficacy of MSCs administration in IBD patients. Although the safety and short-term efficacy of MSCs administration have been evinced, the long-term efficacy of MSCs transplantation has not yet been verified. Herein, we have emphasized the illumination of the therapeutic capacity of MSCs therapy, including naïve MSCs, preconditioned MSCs, and also MSCs-derived exosomes, to alleviate IBD severity in experimental models. Also, a brief overview of published clinical trials in IBD patients has been delivered.
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Affiliation(s)
- Mohamed J. Saadh
- grid.449114.d0000 0004 0457 5303Department of Basic Sciences, Faculty of Pharmacy, Middle East University, Amman, 11831 Jordan
| | - Maria V. Mikhailova
- grid.448878.f0000 0001 2288 8774I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Soheil Rasoolzadegan
- grid.411600.2Department of Surgery, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Falaki
- grid.411600.2Department of Internal Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roozbeh Akhavanfar
- grid.411036.10000 0001 1498 685XSchool of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Amir Rigi
- grid.411463.50000 0001 0706 2472Department of Nursing, Young Researchers and Elite Club, Zahedan Branch, Azad University, Zahedan, Iran
| | - Bahman Abedi Kiasari
- grid.46072.370000 0004 0612 7950Virology Department, Faculty of Veterinary Medicine, The University of Tehran, Tehran, Iran
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36
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Zhou J, Zhang Q, Zhao Y, Song Y, Leng Y, Chen M, Zhou S, Wang Z. The regulatory role of alternative splicing in inflammatory bowel disease. Front Immunol 2023; 14:1095267. [PMID: 37153612 PMCID: PMC10160418 DOI: 10.3389/fimmu.2023.1095267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) mainly includes Crohn's disease and ulcerative colitis. These diseases have a progressive course of chronic relapse and remission and affect a large number of children and adults worldwide. The burden of IBD is rising worldwide, with levels and trends varying greatly in countries and regions. Like most chronic diseases, the costs associated with IBD are high, including hospitalizations, outpatient and emergency visits, surgeries, and pharmacotherapies. However, there is no radical cure for it yet, and its therapeutic targets still need further study. Currently, the pathogenesis of IBD remains unclear. It is generally assumed that the occurrence and development of IBD are related to the environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. Alternative splicing contributes to a various diseases, such as spinal muscular atrophy, liver diseases, and cancers. In the past, it has been reported that alternative splicing events, splicing factors, and splicing mutations were associated with IBD, but there were no reports on the practical application for clinical diagnosis and treatment of IBD using splicing-related methods. Therefore, this article reviews research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
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Affiliation(s)
- Jianli Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Qiao Zhang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuzhen Zhao
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuchen Song
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yanan Leng
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Moxian Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Shaoming Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Zhaoxia Wang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
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Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
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Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
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Djouina M, Waxin C, Leprêtre F, Tardivel M, Tillement O, Vasseur F, Figeac M, Bongiovanni A, Sebda S, Desreumaux P, Launay D, Dubuquoy L, Body-Malapel M, Vignal C. Gene/environment interaction in the susceptibility of Crohn's disease patients to aluminum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158017. [PMID: 35973536 DOI: 10.1016/j.scitotenv.2022.158017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND & AIM The key role of environmental factors in the pathogenesis of Inflammatory Bowel Diseases (IBD) is recognized. Aluminum is suspected to be a risk factor for IBD. However, mechanisms linking aluminum exposure to disease development are unknown. We examined the role of aluminum transport and subcellular localisation on human colon susceptibility to aluminum-induced inflammation. METHODS Human colon biopsies isolated from Crohn's disease (CD) or control patients and Caco-2 cells were incubated with aluminum. The effects of aluminum were evaluated on cytokine secretion and transporter expression. The role of aluminum kinetics parameters was studied in Caco-2 using transport inhibitors and in human colon biopsies by assessing genetic polymorphisms of transporters. RESULTS Aluminum exposure was shown to induce cytokine secretion in colon of CD but not healthy patients. In Caco-2 cells, aluminum internalisation was correlated with inflammatory status. In human colon, analysis of genetic polymorphisms and expression of ABCB1 and SLC26A3 transporters showed that their decreased activity was involved in aluminum-induced inflammation. CONCLUSIONS We hypothesize that alteration in detoxifying response would lead to a deregulation of intestinal homeostasis and to the expression of IBD. Our study emphasizes the complexity of gene/environment interaction for aluminum adverse health effect, highlighting at risk populations or subtypes of patients. A better understanding of correlations between gene expression or SNP and xenobiotic kinetics parameters would shift the medical paradigm to more personalized disease management and treatment.
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Affiliation(s)
- Madjid Djouina
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Christophe Waxin
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Frédéric Leprêtre
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Meryem Tardivel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Olivier Tillement
- Institut Lumière Matière, Université Claude Bernard Lyon 1, CNRS UMR 5306, 69622 Villeurbanne, France
| | - Francis Vasseur
- Univ. Lille, CHU Lille, ULR 2694-METRICS : Évaluation des technologies de santé et des pratiques médicales, F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Antonino Bongiovanni
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Pierre Desreumaux
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Laurent Dubuquoy
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Mathilde Body-Malapel
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France
| | - Cécile Vignal
- Univ. Lille, Inserm, CHU Lille, U1286- INFINITE - Institute for translational research in inflammation, F-59000 Lille, France.
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Gerussi A, Soskic B, Asselta R, Invernizzi P, Gershwin ME. GWAS and autoimmunity: What have we learned and what next. J Autoimmun 2022; 133:102922. [PMID: 36209690 DOI: 10.1016/j.jaut.2022.102922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/07/2022]
Abstract
Autoimmune diseases are common conditions characterized by loss of tolerance, female predominance and a remarkable heterogeneity among different populations. Most often they are polygenic and several genetic loci have been linked with the risk of developing autoimmune diseases. However, causal inference is difficult. When the genomic revolution began there were high hopes of translating fast genetic analyses to the bedside but this has proven to be challenging. Nonetheless, over the last decade, fine-mapping strategies have greatly improved; one of the most significant research lines focuses on the in vivo and ex vivo definition of the effect of genetic variants within the target tissues and within specific subpopulations of immune cells that are involved in the disease pathogenesis. This strategy also includes the longitudinal tracking of a large number of immunophenotypes in many individuals to build a large reference atlas for variant characterization. In this review, we discuss the results obtained by GWAS in autoimmune diseases and review recent advances in fine mapping strategies. More importantly, we discuss gaps and future directions.
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Affiliation(s)
- Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy.
| | - Blagoje Soskic
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Rosanna Asselta
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Merrill E Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
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Wang MY, Wang ZX, Huang LJ, Yang RX, Zou ZY, Ge WS, Ren TY, Fan JG. Premorbid Steatohepatitis Increases the Seriousness of Dextran Sulfate Sodium-induced Ulcerative Colitis in Mice. J Clin Transl Hepatol 2022; 10:847-859. [PMID: 36304494 PMCID: PMC9547267 DOI: 10.14218/jcth.2021.00315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/13/2021] [Accepted: 11/30/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS The concurrence of nonalcoholic steatohepatitis (NASH) and ulcerative colitis (UC) is increasingly seen in clinical practice, but the underlying mechanisms remain unclear. This study aimed to develop a mouse model of the phenomenon by combining high-fat high-cholesterol diet (HFHCD)-induced NASH and dextran sulfate sodium (DSS)-induced UC, that would support mechanistic studies. METHODS Male C57BL/6 mice were randomly assigned to two groups receiving either a chow diet or HFHCD for 12 weeks of NASH modeling. The mice were the divided into four subgroups for UC modeling: (1) A control group given a chow diet with normal drinking water; (2) A colitis group given chow diet with 2% DSS in drinking water; (3) A steatohepatitis group given HFHCD with normal drinking water; and (4) A steatohepatitis + colitis group given HFHCD with 2% DSS in drinking water. RESULTS NASH plus UC had high mortality (58.3%). Neither NASH nor UC alone were fatal. Although DSS-induced colitis did not exacerbate histological liver injury in HFHCD-fed mice, premorbid NASH significantly increased UC-related gut injury compared with UC alone. It was characterized by a significantly shorter colon, more colonic congestion, and a higher histopathological score (p<0.05). Inflammatory (tumor necrosis factor-alpha, interleukin 1 beta, C-C motif chemokine ligand 2, and nuclear factor kappa B) and apoptotic (Bcl2, Bad, Bim, and Bax) signaling pathways were significantly altered in distal colon tissues collected from mice with steatohepatitis + colitis compared with the other experimental groups. CONCLUSIONS Premorbid steatohepatitis significantly aggravated DSS-induced colitis and brought about a lethal phenotype. Potential links between NASH and UC pathogeneses can be investigated using this model.
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Affiliation(s)
- Meng-Yu Wang
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zi-Xuan Wang
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei-Jie Huang
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui-Xu Yang
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zi-Yuan Zou
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen-Song Ge
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tian-Yi Ren
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Correspondence to: Jian-Gao Fan, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China. ORCID: https://orcid.org/0000-0002-8618-6402. Tel: +86-21-25077340, E-mail: ; Tian-Yi Ren, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China. ORCID: https://orcid.org/0000-0002-0844-7072. Tel: +86-18204314931, E-mail:
| | - Jian-Gao Fan
- Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Shanghai, China
- Correspondence to: Jian-Gao Fan, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China. ORCID: https://orcid.org/0000-0002-8618-6402. Tel: +86-21-25077340, E-mail: ; Tian-Yi Ren, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China. ORCID: https://orcid.org/0000-0002-0844-7072. Tel: +86-18204314931, E-mail:
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Fraschilla I, Amatullah H, Rahman RU, Jeffrey KL. Immune chromatin reader SP140 regulates microbiota and risk for inflammatory bowel disease. Cell Host Microbe 2022; 30:1370-1381.e5. [PMID: 36130593 PMCID: PMC10266544 DOI: 10.1016/j.chom.2022.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Inflammatory bowel disease (IBD) is driven by host genetics and environmental factors, including commensal microorganisms. Speckled Protein 140 (SP140) is an immune-restricted chromatin "reader" that is associated with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the disease-causing mechanisms of SP140 remain undefined. Here, we identify an immune-intrinsic role for SP140 in regulating phagocytic defense responses to prevent the expansion of inflammatory bacteria. Mice harboring altered microbiota due to hematopoietic Sp140 deficiency exhibited severe colitis that was transmissible upon cohousing and ameliorated with antibiotics. Loss of SP140 results in blooms of Proteobacteria, including Helicobacter in Sp140-/- mice and Enterobacteriaceae in humans bearing the CD-associated SP140 loss-of-function variant. Phagocytes from patients with the SP140 loss-of-function variant and Sp140-/- mice exhibited altered antimicrobial defense programs required for control of pathobionts. Thus, mutations within this epigenetic reader may constitute a predisposing event in human diseases provoked by microbiota.
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Affiliation(s)
- Isabella Fraschilla
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Raza-Ur Rahman
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Massachusetts Institute of Technology Center for Microbiome, Informatics and Therapeutics, Cambridge, MA 02139, USA.
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Cázares-Olivera M, Miroszewska D, Hu L, Kowalski J, Jaakkola UM, Salminen S, Li B, Yatkin E, Chen Z. Animal unit hygienic conditions influence mouse intestinal microbiota and contribute to T-cell-mediated colitis. Exp Biol Med (Maywood) 2022; 247:1752-1763. [PMID: 35946176 PMCID: PMC9638955 DOI: 10.1177/15353702221113826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders of the gastrointestinal tract with worldwide increasing incidence. Recent studies indicate that certain species of intestinal bacteria are strongly associated with IBD. Helper T lymphocytes are not only the key players in mediating host defense against a wide variety of pathogens but also contribute to pathogenesis of many immune-related diseases. Here, using the T cell transfer model of colitis, we observed that the mice maintained in a specific-pathogen free (SPF) unit after receiving naïve CD4+ T cells developed mild disease. The same mice developed different degrees of disease when they were maintained in a conventional animal facility (non-SPF), where some pathogens were detected during routine health monitoring. Consistently, increased circulating inflammatory cytokines as well as Th1 and Th17 cells were detected in mice housed in non-SPF units. 16S rRNA sequencing of feces samples enabled us to identify changes in the microbiota composition of mice kept in different facilities. Our data indicate that environmental factors influence gut microbiota composition of mice, leading to development of colitis in a T-cell-dependent manner. In conclusion, changes in environmental conditions and microbial status of experimental animals appear to contribute to progression of colitis.
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Affiliation(s)
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, 80-307 Gdańsk, Poland
| | - Lili Hu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, Finland
| | - Jacek Kowalski
- Department of Pathomorphology, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Ulla-Marjut Jaakkola
- Central Animal Laboratory, Faculty of Medicine, University of Turku (UTUCAL), 20520 Turku, Finland
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20520 Turku, Finland
| | - Bin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200085, China
| | - Emrah Yatkin
- Central Animal Laboratory, Faculty of Medicine, University of Turku (UTUCAL), 20520 Turku, Finland
| | - Zhi Chen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, Finland,Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, 80-307 Gdańsk, Poland,Zhi Chen.
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Olaisen M, Richard ML, Beisvåg V, Granlund AVB, Røyset ES, Rué O, Martinsen TC, Sandvik AK, Sokol H, Fossmark R. The ileal fungal microbiota is altered in Crohn's disease and is associated with the disease course. Front Med (Lausanne) 2022; 9:868812. [PMID: 36237548 PMCID: PMC9551188 DOI: 10.3389/fmed.2022.868812] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Fungal microbiota's involvement in the pathogenesis of Crohn's disease (CD) is incompletely understood. The terminal ileum is a predilection site both for primary involvement and recurrences of CD. We, therefore, assessed the mucosa-associated mycobiota in the inflamed and non-inflamed ileum in patients with CD. Methods The mucosa-associated mycobiota was assessed by ITS2 sequencing in a total of 168 biopsies sampled 5 and 15 cm proximal of the ileocecal valve or ileocolic anastomosis in 44 CD patients and 40 healthy controls (HC). CD patients with terminal ileitis, with endoscopic inflammation at 5 cm and normal mucosa at 15 cm and no history of upper CD involvement, were analyzed separately. The need for additional CD treatment the year following biopsy collection was recorded. Results CD patients had reduced mycobiota evenness, increased Basidiomycota/Ascomycota ratio, and reduced abundance of Chytridiomycota compared to HC. The mycobiota of CD patients were characterized by an expansion of Malassezia and a depletion of Saccharomyces, along with increased abundances of Candida albicans and Malassezia restricta. Malassezia was associated with the need for treatment escalation during follow-up. Current anti-TNF treatment was associated with lower abundances of Basidiomycota. The alpha diversity of the inflamed and proximal non-inflamed mucosa within the same patients was similar. However, the inflamed mucosa had a more dysbiotic composition with increased abundances of Candida sake and reduced abundances of Exophiala equina and Debaryomyces hansenii. Conclusions The ileal mucosa-associated mycobiota in CD patients is altered compared to HC. The mycobiota in the inflamed and proximal non-inflamed ileum within the same patients harbor structural differences which may play a role in the CD pathogenesis. Increased abundance of Malassezia was associated with an unfavorable disease course.
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Affiliation(s)
- Maya Olaisen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav's Hospital - Trondheim University Hospital, Trondheim, Norway
| | - Mathias L. Richard
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Vidar Beisvåg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Central Administration, St. Olav's Hospital - Trondheim University Hospital, Trondheim, Norway
| | - Atle van Beelen Granlund
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Elin S. Røyset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Pathology, St. Olav's Hospital - Trondheim University Hospital, Trondheim, Norway
| | - Olivier Rué
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - Tom Christian Martinsen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav's Hospital - Trondheim University Hospital, Trondheim, Norway
| | - Arne Kristian Sandvik
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav's Hospital - Trondheim University Hospital, Trondheim, Norway
- Centre of Molecular Inflammation Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Harry Sokol
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
- Gastroenterology Department, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Sorbonne Université, Paris, France
| | - Reidar Fossmark
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, St. Olav's Hospital - Trondheim University Hospital, Trondheim, Norway
- *Correspondence: Reidar Fossmark
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Ianiri G, LeibundGut-Landmann S, Dawson TL. Malassezia: A Commensal, Pathogen, and Mutualist of Human and Animal Skin. Annu Rev Microbiol 2022; 76:757-782. [PMID: 36075093 DOI: 10.1146/annurev-micro-040820-010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Identified in the late nineteenth century as a single species residing on human skin, Malassezia is now recognized as a diverse genus comprising 18 species inhabiting not only skin but human gut, hospital environments, and even deep-sea sponges. All cultivated Malassezia species are lipid dependent, having lost genes for lipid synthesis and carbohydrate metabolism. The surging interest in Malassezia results from development of tools to improve sampling, culture, identification, and genetic engineering, which has led to findings implicating it in numerous skin diseases, Crohn disease, and pancreatic cancer. However, it has become clear that Malassezia plays a multifaceted role in human health, with mutualistic activity in atopic dermatitis and a preventive effect against other skin infections due to its potential to compete with skin pathogens such as Candida auris. Improved understanding of complex microbe-microbe and host-microbe interactions will be required to define Malassezia's role in human and animal health and disease so as to design targeted interventions.
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Affiliation(s)
- Giuseppe Ianiri
- Department of Agricultural, Environmental, and Food Sciences, University of Molise, Campobasso, Italy
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Faculty of Vetsuisse, and Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Thomas L Dawson
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore; .,Department of Drug Discovery, College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina, USA
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Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O'Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility. Nat Genet 2022; 54:1275-1283. [PMID: 36038634 PMCID: PMC9700438 DOI: 10.1038/s41588-022-01156-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/12/2022] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls. We directly implicate ten genes in general onset CD for the first time to our knowledge via association to coding variation, four of which lie within established CD GWAS loci. In nine instances, a single coding variant is significantly associated, and in the tenth, ATG4C, we see additionally a significantly increased burden of very rare coding variants in CD cases. In addition to reiterating the central role of innate and adaptive immune cells as well as autophagy in CD pathogenesis, these newly associated genes highlight the emerging role of mesenchymal cells in the development and maintenance of intestinal inflammation.
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Affiliation(s)
- Aleksejs Sazonovs
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Christine R Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kai Yuan
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brandon Avila
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria T Abreu
- Crohn's and Colitis Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Matthieu Allez
- Hopital Saint-Louis, APHP, Universite de Paris, INSERM U1160, Paris, France
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Crohn's and Colitis Center, Massachusetts General Hospital, Boston, MA, USA
| | - Gil Atzmon
- Department for Human Biology, University of Haifa, Haifa, Israel
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- The Institute for Aging Research, The Nathan Shock Center of Excellence in the Basic Biology of Aging and the Paul F. Glenn Center for the Biology of Human Aging Research at Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - Laurent Beaugerie
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Ashley Beecham
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Alain Bitton
- McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Bernd Bokemeyer
- Department of Internal Medicine, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrew Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA
| | | | | | - Jacques Cosnes
- Professeur Chef de Service chez APHP and Universite Paris-6, Paris, France
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Allan Daly
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noor Dawany
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcella Devoto
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
- University of Rome Sapienza, Rome, Italy
- IRGB - CNR, Cagliari, Italy
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eva Ellinghaus
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Laura Fachal
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | | | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tian Ge
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kyle Gettler
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mamta Giri
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Philippe Goyette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Daniel Graham
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | | | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marc Hoeppner
- Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Peter Irving
- Department of Gastroenterology, Guys and Saint Thomas Hospital, London, UK
- School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Vivek Iyer
- Human Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Chaim Jalas
- Director of Genetic Resources and Services, Center for Rare Jewish Genetic Disorders, Bonei Olam, Brooklyn, NY, USA
| | - Judith Kelsen
- Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Hamed Khalili
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Barbara S Kirschner
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Kimmo Kontula
- Department of Medicine, Helsinki University Hospital, and Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Jukka T Koskela
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Subra Kugathasan
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Chloé Lévesque
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | | | - James D Lewis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Crohn's and Colitis Foundation, New York, NY, USA
| | | | - Britt-Sabina Loescher
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | | | - John Mansfield
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sandra May
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Myriam Mni
- University of Liège, ULG, Liège, Belgium
| | | | | | | | | | - David T Okou
- Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
- Institut National de Sante Publique (INSP), Abidjan, Côte d'Ivoire
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Harry Ostrer
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aarno Palotie
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Jean Paquette
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
| | - Joel Pekow
- Department of Gastroenterology, University of Chicago Medicine, Chicago, IL, USA
| | - Inga Peter
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marieke J Pierik
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | | | - Natalie Prescott
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - Ann E Pulver
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Daniel L Rice
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Bruce Sands
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Stefan Schreiber
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - L Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | | | - Philippe Seksik
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Rasha Shawky
- IBD BioResource, NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Alison Simmons
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jurgita Skeiceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Universite, Saint Antoine Hospital, Paris, France
| | - Matthew Solomonson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hari Somineni
- Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Stephan Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Turner
- Shaare Zedek Medical Center, Jerusalem, Israel
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Biomedical Research Centre, Nuffield Department of Clinical Medicine, Experimental Medicine Division, University of Oxford, Oxford, UK
- Department of Pediatrics, John Radcliffe Hospital, Oxford, UK
| | - Andrea E van der Meulen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Séverine Vermeire
- University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Sare Verstockt
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Andre Franke
- Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Steven R Brant
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Crohn's Colitis Center of New Jersey, Department of Medicine, Rutgers Robert Wood Johnson Medical School and Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, New Brunswick and Piscataway, NJ, USA
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Kurt Isselbacher Professor of Medicine at Harvard Medical School, Cambridge, MA, USA
- Core Institute Member, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Immunology Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John D Rioux
- Research Center Montreal Heart Institute, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Carl A Anderson
- Genomics of Inflammation and Immunity Group, Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Mark J Daly
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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Ashton JJ, Seaby EG, Beattie RM, Ennis S. NOD2 in Crohn's disease- unfinished business. J Crohns Colitis 2022; 17:450-458. [PMID: 36006803 PMCID: PMC10069614 DOI: 10.1093/ecco-jcc/jjac124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 01/01/2023]
Abstract
Studies of Crohn's disease consistently implicate NOD2 as the most important gene in disease pathogenesis since first being identified in 2001. Since this point, genome-wide association, next-generation sequencing, and functional analyses have all confirmed a key role for NOD2, but despite this, NOD2 also has significant unresolved complexity. More recent studies have reinvigorated an early hypothesis that NOD2 may be a single-gene cause of disease, and the distinct ileal stricturing phenotype seen with NOD2-related disease presents an opportunity for personalised diagnosis, disease prediction and targeted therapy. The genomics of NOD2 has much that remains unknown, including the role of rare variation, phasing of variants across the haplotype block and the role of variation in the NOD2-regulatory regions. Here, we discuss the evidence and the unmet needs of NOD2-research, based on recently published evidence, and suggest methods that may meet these requirements.
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Affiliation(s)
- James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Eleanor G Seaby
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Kang YH, Tucker SA, Quevedo SF, Inal A, Korzenik JR, Haigis MC. Metabolic analyses reveal dysregulated NAD+ metabolism and altered mitochondrial state in ulcerative colitis. PLoS One 2022; 17:e0273080. [PMID: 35976971 PMCID: PMC9385040 DOI: 10.1371/journal.pone.0273080] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Ulcerative colitis (UC) is a complex, multifactorial disease driven by a dysregulated immune response against host commensal microbes. Despite rapid advances in our understanding of host genomics and transcriptomics, the metabolic changes in UC remain poorly understood. We thus sought to investigate distinguishing metabolic features of the UC colon (14 controls and 19 patients). Metabolomics analyses revealed inflammation state as the primary driver of metabolic variation rather than diagnosis, with multiple metabolites differentially regulated between inflamed and uninflamed tissues. Specifically, inflamed tissues were characterized by reduced levels of nicotinamide adenine dinucleotide (NAD+) and enhanced levels of nicotinamide (NAM) and adenosine diphosphate ribose (ADPr). The NAD+/NAM ratio, which was reduced in inflamed patients, served as an effective classifier for inflammation in UC. Mitochondria were also structurally altered in UC, with UC patient colonocytes displaying reduced mitochondrial density and number. Together, these findings suggest a link between mitochondrial dysfunction, inflammation, and NAD+ metabolism in UC.
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Affiliation(s)
- Yu Hui Kang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, MA, United States of America
| | - Sarah A. Tucker
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
| | - Silvia F. Quevedo
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Aslihan Inal
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
| | - Joshua R. Korzenik
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Marcia C. Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
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Vogeley C, Nguyen T, Woeste S, Krutmann J, Haarmann-Stemmann T, Rossi A. Rapid and simple analysis of short and long sequencing reads using DuesselporeTM. Front Genet 2022; 13:931996. [PMID: 36035127 PMCID: PMC9403543 DOI: 10.3389/fgene.2022.931996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 12/11/2022] Open
Abstract
Transcriptome analysis experiments enable researchers to gain extensive insights into the molecular mechanisms underlying cell physiology and disease. Oxford Nanopore Technologies (ONT) has recently been developed as a fast, miniaturized, portable, and cost-effective alternative to next-generation sequencing (NGS). However, RNA-Seq data analysis software that exploits ONT portability and allows scientists to easily analyze ONT data everywhere without bioinformatics expertise is not widely available. We developed DuesselporeTM, an easy-to-follow deep sequencing workflow that runs as a local webserver and allows the analysis of ONT data everywhere without requiring additional bioinformatics tools or internet connection. DuesselporeTM output includes differentially expressed genes and further downstream analyses, such as variance heatmap, disease and gene ontology plots, gene concept network plots, and exports customized pathways for different cellular processes. We validated DuesselporeTM by analyzing the transcriptomic changes induced by PCB126, a dioxin-like PCB, and a potent aryl hydrocarbon receptor (AhR) agonist in human HaCaT keratinocytes, a well-characterized model system. DuesselporeTM was specifically developed to analyze ONT data, but we also implemented NGS data analysis. DuesselporeTM is compatible with Linux, Microsoft, and Mac operating systems and allows convenient, reliable, and cost-effective analysis of ONT and NGS data.
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49
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Main human inborn errors of immunity leading to fungal infections. Clin Microbiol Infect 2022; 28:1435-1440. [PMID: 35863627 DOI: 10.1016/j.cmi.2022.06.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 01/23/2023]
Abstract
BACKGROUND The host molecular and genetic features are essential in providing susceptibility to a broad spectrum of fungal infections; most of these do not cause disease in healthy individuals because of mutual benefits with opportunistic fungi besides the host's capacity to control the infections. In contrast, patients with primary immunodeficiency (PID) can develop mild superficial to life-threatening invasive infections. In the last years, thanks to next-generation sequencing (NGS), several inborn-error variants have been discovered in genes encoding protein acting against fungal infections, contributing to better defining the role of innate and adaptive immunity cooperation during infection resolution. Candida fungal infection, that sometimes-striking healthy subjects, is responsible for the chronic mucocutaneous candidiasis (CMC) that is one of the principal clinical manifestations occurring in several rare PIDs associated with an inborn error of IL17-immunity. OBJECTIVE This review aimed to provide an overview of CMC-derived genetic defects, including IL17-deficiencies (IL17A, IL17F, IL17RA, IL17RC), STAT1 gain-of-function (GOF)- deficiency, STAT3-HIES and CARD9-deficiency. SOURCES We carried out detailed research work to identify interesting articles, commentaries, and reviews in the PubMed literature to ensure a correct and updated for this narrative review. CONTENT We propose an in-depth description and an update of genetic and cellular mechanisms underlying fungal infections, focusing on the IL17-mediated response, a report of clinical manifestations and describe therapeutic options. IMPLICATION This narrative review will help clinician to identify the correct management of patients based on molecular and cellular findings underlying pathogenic mechanisms of different IEIs. Moreover achieve the genetic diagnosis will be useful to offer genetic counselling intra- and inter-family and to ensure a personalized treatment of patients.
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Basmanav FB, Betz RC. Translational impact of omics studies in alopecia areata: recent advances and future perspectives. Expert Rev Clin Immunol 2022; 18:845-857. [PMID: 35770930 DOI: 10.1080/1744666x.2022.2096590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Alopecia areata (AA) is a non-scarring, hair loss disorder and a common autoimmune-mediated disease with an estimated lifetime risk of about 2%. To date, the treatment of AA is mainly based on suppression or stimulation of the immune response. Genomics and transcriptomics studies generated important insights into the underlying pathophysiology, enabled discovery of molecular disease signatures, which were used in some of the recent clinical trials to monitor drug response and substantiated the consideration of new therapeutic modalities for the treatment of AA such as abatacept, dupilumab, ustekinumab and Janus Kinase (JAK) inhibitors. AREAS COVERED In this review, genomics and transcriptomics studies in AA are discussed in detail with particular emphasis on their past and prospective translational impacts. Microbiome studies are also briefly introduced. EXPERT OPINION The generation of large datasets using the new high-throughput technologies has revolutionized medical research and AA has also benefited from the wave of omics studies. However, the limitations associated with JAK inhibitors and clinical heterogeneity in AA patients underscore the necessity for continuing omics research in AA for discovery of novel therapeutic modalities and development of clinical tools for precision medicine.
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Affiliation(s)
- F Buket Basmanav
- Medical Faculty & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Regina C Betz
- Medical Faculty & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
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