1
|
Gaba K, Malhotra P, Kumar A, Suneja P, Dang AS. Understanding the Genetic Basis of Celiac Disease: A Comprehensive Review. Cell Biochem Biophys 2024:10.1007/s12013-024-01371-0. [PMID: 38907939 DOI: 10.1007/s12013-024-01371-0] [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] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Celiac disease is an immune-mediated enteropathy with typical symptoms of weight loss, abdominal bloating, diarrhea, vomiting, or constipation. Many shreds of evidence show that CeD is hereditary in origin and various biochemical pathways have been connected to its etiology. Numerous genes from different physiological pathways have been investigated in the last few decades, however a comprehensive analysis is required to address the gaps and provide a more integrated understanding of how these genetic factors contribute to the pathogenesis of disease. Present study attempts to summarize the historical and up-to-date findings to understand the role of genetics in Celiac disease. The literature was searched from sources such as PubMed and Google Scholar to analyze studies conducted on celiac disease from the years 1995 to 2024. Term maps were created to examine the frequency of studies related to various terms to understand the major focus of the studies till date. The study also concise the different genetic polymorphisms studied in a table to understand the role of genetics in celiac diseases. Early studies on celiac disease primarily focused on its pathophysiology, prevalence, and general aspects, with limited attention to genetics. However, recent studies have increasingly emphasized the genetic basis of the disease and highlighting the involvement of various pathways like inflammation, T-cell differentiation and activation, epithelial barrier function, stress and apoptosis pathways. However, present study indicate that most current research predominantly focus on cytokines, specifically the TNF alpha gene. Consequently, there is a need for additional research to gain a more comprehensive understanding of the genetics of celiac disease.
Collapse
Affiliation(s)
- Kajal Gaba
- Centre For Medical Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | | | - Anil Kumar
- Centre For Medical Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Pooja Suneja
- Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, India
| | - Amita Suneja Dang
- Centre For Medical Biotechnology, Maharshi Dayanand University, Rohtak, 124001, India.
| |
Collapse
|
2
|
Cao G, Luo Q, Wu Y, Chen G. Inflammatory bowel disease and rheumatoid arthritis share a common genetic structure. Front Immunol 2024; 15:1359857. [PMID: 38938570 PMCID: PMC11208460 DOI: 10.3389/fimmu.2024.1359857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Background The comorbidity rate of inflammatory bowel disease (IBD) and rheumatoid arthritis (RA) is high; nevertheless, the reasons behind this high rate remain unclear. Their similar genetic makeup probably contributes to this comorbidity. Methods Based on data obtained from the genome-wide association study of IBD and RA, we first assessed an overall genetic association by performing the linkage disequilibrium score regression (LDSC) analysis. Further, a local correlation analysis was performed by estimating the heritability in summary statistics. Next, the causality between the two diseases was analyzed by two-sample Mendelian randomization (MR). A genetic overlap was analyzed by the conditional/conjoint false discovery rate (cond/conjFDR) method.LDSC with specific expression of gene analysis was performed to identify related tissues between the two diseases. Finally, GWAS multi-trait analysis (MTAG) was also carried out. Results IBD and RA are correlated at the genomic level, both overall and locally. The MR results suggested that IBD induced RA. We identified 20 shared loci between IBD and RA on the basis of a conjFDR of <0.01. Additionally, we identified two tissues, namely spleen and small intestine terminal ileum, which were commonly associated with both IBD and RA. Conclusion Herein, we proved the presence of a polygenic overlap between the genetic makeup of IBD and RA and provided new insights into the genetic architecture and mechanisms underlying the high comorbidity between these two diseases.
Collapse
Affiliation(s)
- Guoling Cao
- Department of Anorectal Surgery, The People’s Hospital of Cangnan, Wenzhou, China
| | - Qinghua Luo
- Clinical Medical College, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yunxiang Wu
- Department of Anorectal Surgery, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
| | - Guanghua Chen
- Department of Anorectal Surgery, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, China
| |
Collapse
|
3
|
Tsygankov AY. Role of Tula-Family Proteins in Cell Signaling and Activation: Advances and Challenges. Int J Mol Sci 2024; 25:4434. [PMID: 38674019 PMCID: PMC11050124 DOI: 10.3390/ijms25084434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
This Special Issue entitled "Role of Tula-Family Proteins in Cell Signaling and Activation: Advances and Challenges" is focused on a relatively novel vertebrate gene/protein family termed alternatively TULA, UBASH3, or STS [...].
Collapse
Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| |
Collapse
|
4
|
Skoracka K, Hryhorowicz S, Tovoli F, Raiteri A, Rychter AM, Słomski R, Dobrowolska A, Granito A, Krela-Kaźmierczak I. From an understanding of etiopathogenesis to novel therapies-what is new in the treatment of celiac disease? Front Pharmacol 2024; 15:1378172. [PMID: 38698821 PMCID: PMC11063403 DOI: 10.3389/fphar.2024.1378172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Celiac disease, a chronic autoimmune disorder caused by genetic factors and exposure to gluten, is increasingly being recognized and diagnosed in both children and adults. Scientists have been searching for a cure for this disease for many years, but despite the impressive development of knowledge in this field, a gluten-free diet remains the only recommended therapy for all patients. At the same time, the increasing diagnosis of celiac disease in adults, which was considered a childhood disease in the 20th century, has opened a discussion on the etiopathology of the disease, which is proven to be very complex and involves genetic, immunological, nutritional, environmental and gut microbiota-related factors. In this review, we extensively discuss these factors and summarize the knowledge of the proposed state-of-the-art treatments for celiac disease to address the question of whether a better understanding of the etiopathogenesis of celiac disease has opened new directions for therapy.
Collapse
Affiliation(s)
- Kinga Skoracka
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Francesco Tovoli
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Alberto Raiteri
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Anna Maria Rychter
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Nutrigenetics, Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alessandro Granito
- Division of Internal Medicine, Hepatobiliary and Immunoallergic Diseases, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Nutrigenetics, Department of Gastroenterology, Dietetics and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| |
Collapse
|
5
|
Wang J, Wang C, Hu A, Yu K, Kuang Y, Gajendran B, Zacksenhaus E, Sample KM, Xiao X, Liu W, Ben-David Y. FLI1 induces erythroleukemia through opposing effects on UBASH3A and UBASH3B expression. BMC Cancer 2024; 24:326. [PMID: 38461240 PMCID: PMC10925000 DOI: 10.1186/s12885-024-12075-2] [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: 07/21/2023] [Accepted: 03/01/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND FLI1 is an oncogenic transcription factor that promotes diverse malignancies through mechanisms that are not fully understood. Herein, FLI1 is shown to regulate the expression of Ubiquitin Associated and SH3 Domain Containing A/B (UBASH3A/B) genes. UBASH3B and UBASH3A are found to act as an oncogene and tumor suppressor, respectively, and their combined effect determines erythroleukemia progression downstream of FLI1. METHODS Promoter analysis combined with luciferase assays and chromatin immunoprecipitation (ChIP) analysis were applied on the UBASH3A/B promoters. RNAseq analysis combined with bioinformatic was used to determine the effect of knocking-down UBASH3A and UBASH3B in leukemic cells. Downstream targets of UBASH3A/B were inhibited in leukemic cells either via lentivirus-shRNAs or small molecule inhibitors. Western blotting and RT-qPCR were used to determine transcription levels, MTT assays to assess proliferation rate, and flow cytometry to examine apoptotic index. RESULTS Knockdown of FLI1 in erythroleukemic cells identified the UBASH3A/B genes as potential downstream targets. Herein, we show that FLI1 directly binds to the UBASH3B promoter, leading to its activation and leukemic cell proliferation. In contrast, FLI1 indirectly inhibits UBASH3A transcription via GATA2, thereby antagonizing leukemic growth. These results suggest oncogenic and tumor suppressor roles for UBASH3B and UBASH3A in erythroleukemia, respectively. Mechanistically, we show that UBASH3B indirectly inhibits AP1 (FOS and JUN) expression, and that its loss leads to inhibition of apoptosis and acceleration of proliferation. UBASH3B also positively regulates the SYK gene expression and its inhibition suppresses leukemia progression. High expression of UBASH3B in diverse tumors was associated with worse prognosis. In contrast, UBASH3A knockdown in erythroleukemic cells increased proliferation; and this was associated with a dramatic induction of the HSP70 gene, HSPA1B. Accordingly, knockdown of HSPA1B in erythroleukemia cells significantly accelerated leukemic cell proliferation. Accordingly, overexpression of UBASH3A in different cancers was predominantly associated with good prognosis. These results suggest for the first time that UBASH3A plays a tumor suppressor role in part through activation of HSPA1B. CONCLUSIONS FLI1 promotes erythroleukemia progression in part by modulating expression of the oncogenic UBASH3B and tumor suppressor UBASH3A.
Collapse
MESH Headings
- Humans
- Leukemia, Erythroblastic, Acute/genetics
- Leukemia, Erythroblastic, Acute/pathology
- Proto-Oncogene Protein c-fli-1/genetics
- Proto-Oncogene Protein c-fli-1/metabolism
- RNA, Small Interfering/genetics
- Genes, Tumor Suppressor
- Gene Expression Regulation
- Gene Expression Regulation, Neoplastic
- Cell Line, Tumor
- Oncogene Proteins, Fusion/genetics
- RNA-Binding Protein EWS/genetics
- Adaptor Proteins, Signal Transducing/metabolism
Collapse
Affiliation(s)
- Jie Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China
| | - Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China
| | - Kunlin Yu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China
| | - Yi Kuang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guizhou Province, Guiyang, 550025, People's Republic of China
| | - Eldad Zacksenhaus
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Advanced Diagnostics, Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Xiao Xiao
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China.
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China.
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang-550014, Guizhou, People's Republic of China.
- Natural Products Research Center of Guizhou Province, High Tech Zone, Province Science City, Baiyun District, Guiyang, 550014, China.
| |
Collapse
|
6
|
Cho J, Kim J, Song JS, Uh Y, Lee JH, Lee HS. Whole-Exome Sequencing and Analysis of the T Cell Receptor β and γ Repertoires in Rheumatoid Arthritis. Diagnostics (Basel) 2024; 14:529. [PMID: 38473001 DOI: 10.3390/diagnostics14050529] [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: 01/22/2024] [Revised: 02/23/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
This study investigated the potential genetic variants of rheumatoid arthritis (RA) using whole-exome sequencing (WES) and evaluated the disease course using T cell receptor (TCR) repertoire analysis. Fourteen patients with RA and five healthy controls (HCs) were enrolled. For the RA patient group, only treatment-naïve patients were recruited, and data were collected at baseline as well as at 6 and 12 months following the initiation of the disease-modifying antirheumatic drug (DMARD) treatment. Laboratory data and disease parameters were also collected. Genetic variants were detected using WES, and the diversity of the TCR repertoire was assessed using the Shannon-Wiener diversity index. While some variants were detected by WES, their clinical significance should be confirmed by further studies. The diversity of the TCR repertoire in the RA group was lower than that in the HCs; however, after DMARD treatment, it increased significantly. The diversity was negatively correlated with the laboratory findings and disease measures with statistical significance. Variants with a potential for RA pathogenesis were identified, and the clinical significance of the TCR repertoire was evaluated in Korean patients with RA. Further studies are required to confirm the findings of the present study.
Collapse
Affiliation(s)
- Jooyoung Cho
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Juwon Kim
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Ju Sun Song
- GC Genome, GC Labs, Yongin 16924, Republic of Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Jong-Han Lee
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Hyang Sun Lee
- Division of Rheumatology, Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| |
Collapse
|
7
|
Vukojević K, Šoljić V, Martinović V, Raguž F, Filipović N. The Ubiquitin-Associated and SH3 Domain-Containing Proteins (UBASH3) Family in Mammalian Development and Immune Response. Int J Mol Sci 2024; 25:1932. [PMID: 38339213 PMCID: PMC10855836 DOI: 10.3390/ijms25031932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
UBASH3A and UBASH3B are protein families of atypical protein tyrosine phosphatases that function as regulators of various cellular processes during mammalian development. As UBASH3A has only mild phosphatase activity, its regulatory effects are based on the phosphatase-independent mechanisms. On the contrary, UBASH3B has strong phosphatase activity, and the suppression of its receptor signalling is mediated by Syk and Zap-70 kinases. The regulatory functions of UBASH3A and UBASH3B are particularly evident in the lymphoid tissues and kidney development. These tyrosine phosphatases are also known to play key roles in autoimmunity and neoplasms. However, their involvement in mammalian development and its regulatory functions are largely unknown and are discussed in this review.
Collapse
Affiliation(s)
- Katarina Vukojević
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia;
- Department of Anatomy, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- Department of Histology and Embryology, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
- Faculty of Health Studies, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- Center for Translational Research in Biomedicine, University of Split School of Medicine, 21000 Split, Croatia
| | - Violeta Šoljić
- Department of Histology and Embryology, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
- Faculty of Health Studies, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
| | - Vlatka Martinović
- Department of Surgery, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
| | - Fila Raguž
- Department of Internal Medicine, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina;
| | - Natalija Filipović
- Department of Anatomy, Histology and Embryology, University of Split School of Medicine, 21000 Split, Croatia;
- Department of Anatomy, School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- Center for Translational Research in Biomedicine, University of Split School of Medicine, 21000 Split, Croatia
| |
Collapse
|
8
|
Ponce-de-León C, Lorite P, López-Casado MÁ, Mora P, Palomeque T, Torres MI. Expression of Elafin and CD200 as Immune Checkpoint Molecules Involved in Celiac Disease. Int J Mol Sci 2024; 25:852. [PMID: 38255930 PMCID: PMC10815464 DOI: 10.3390/ijms25020852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/31/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
We comprehensively evaluated the expression of therapeutically targetable immune checkpoint molecules involved in celiac disease (CD). We have focused on the alteration of the CD200/CD200R pathway and Elafin expression in celiac disease and discussed their roles in regulating the immune response. There are limited data related to the expression or function of these molecules in celiac disease. This finding could significantly contribute to the understanding of the clinical manifestation of CD. CD200, CD200R and Elafin distributions were determined by ELISA and immunohistochemistry analyses in serum and biopsies of CD patients. Analyses of Th1 and Th17 cytokines were determined. PCR amplification of a fragment of the PI3 gene was carried out using genomic DNA isolated from whole blood samples of the study subjects. Different aliquots of the PCR reaction product were subjected to RFLP analysis for SNP genotyping and detection. We characterized the expression and function of the CD200-CD200R axis and PI3 in celiac disease. A significantly higher level of soluble CD200 and CD200R and lower expression of PI3 in serum of CD patients was observed compared to healthy controls. Consistent with our results, CD200 expression is regulated by IFN-gamma. Interaction of CD200/CD200R leads to production of type-Th1 and -Th17 cytokines. Regarding the PI3 genotype, the CT genotype proportion SNP rs1733103 and the GG genotype SNP rs41282752 were predominant in CD patients. SNP rs1733103 showed a significant association between the SNP variables and CD. In celiac disease the immune checkpoint is compromised or dysregulated, which can contribute to inflammation and the autoimmunity process. The study of these checkpoint points will lead to the development of targeted therapies aimed at restoring immunological balance in CD. Specific coding regions of the PI3 gene-splice variants predispose the Elafin protein, both at the transcriptional and post-translational levels, to modify its expression and function, resulting in reduced differential functional protein levels in patients with active celiac disease.
Collapse
Affiliation(s)
- Candelaria Ponce-de-León
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (C.P.-d.-L.); (P.L.); (P.M.); (T.P.)
| | - Pedro Lorite
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (C.P.-d.-L.); (P.L.); (P.M.); (T.P.)
| | | | - Pablo Mora
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (C.P.-d.-L.); (P.L.); (P.M.); (T.P.)
| | - Teresa Palomeque
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (C.P.-d.-L.); (P.L.); (P.M.); (T.P.)
| | - María Isabel Torres
- Department of Experimental Biology, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (C.P.-d.-L.); (P.L.); (P.M.); (T.P.)
| |
Collapse
|
9
|
Tsygankov AY. TULA Proteins in Men, Mice, Hens, and Lice: Welcome to the Family. Int J Mol Sci 2023; 24:ijms24119126. [PMID: 37298079 DOI: 10.3390/ijms24119126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The two members of the UBASH3/STS/TULA protein family have been shown to critically regulate key biological functions, including immunity and hemostasis, in mammalian biological systems. Negative regulation of signaling through immune receptor tyrosine-based activation motif (ITAM)- and hemITAM-bearing receptors mediated by Syk-family protein tyrosine kinases appears to be a major molecular mechanism of the down-regulatory effect of TULA-family proteins, which possess protein tyrosine phosphatase (PTP) activity. However, these proteins are likely to carry out some PTP-independent functions as well. Whereas the effects of TULA-family proteins overlap, their characteristics and their individual contributions to cellular regulation also demonstrate clearly distinct features. Protein structure, enzymatic activity, molecular mechanisms of regulation, and biological functions of TULA-family proteins are discussed in this review. In particular, the usefulness of the comparative analysis of TULA proteins in various metazoan taxa, for identifying potential roles of TULA-family proteins outside of their functions already established in mammalian systems, is examined.
Collapse
Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| |
Collapse
|
10
|
Newman JRB, Concannon P, Ge Y. UBASH3A Interacts with PTPN22 to Regulate IL2 Expression and Risk for Type 1 Diabetes. Int J Mol Sci 2023; 24:ijms24108671. [PMID: 37240014 DOI: 10.3390/ijms24108671] [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: 03/31/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
UBASH3A is a negative regulator of T cell activation and IL-2 production and plays key roles in autoimmunity. Although previous studies revealed the individual effects of UBASH3A on risk for type 1 diabetes (T1D; a common autoimmune disease), the relationship of UBASH3A with other T1D risk factors remains largely unknown. Given that another well-known T1D risk factor, PTPN22, also inhibits T cell activation and IL-2 production, we investigated the relationship between UBASH3A and PTPN22. We found that UBASH3A, via its Src homology 3 (SH3) domain, physically interacts with PTPN22 in T cells, and that this interaction is not altered by the T1D risk coding variant rs2476601 in PTPN22. Furthermore, our analysis of RNA-seq data from T1D cases showed that the amounts of UBASH3A and PTPN22 transcripts exert a cooperative effect on IL2 expression in human primary CD8+ T cells. Finally, our genetic association analyses revealed that two independent T1D risk variants, rs11203203 in UBASH3A and rs2476601 in PTPN22, interact statistically, jointly affecting risk for T1D. In summary, our study reveals novel interactions, both biochemical and statistical, between two independent T1D risk loci, and suggests how these interactions may affect T cell function and increase risk for T1D.
Collapse
Affiliation(s)
- Jeremy R B Newman
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Patrick Concannon
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yan Ge
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| |
Collapse
|
11
|
Abdelrahman AH, Ibrahim AA, Eid OM, Hassan M, Eid MM, Nour El Din Abd El Baky AM, Ismail M, Abou-Zekri M, Abd El-Fattah SN. A pilot study on promoter methylation of MTHFR, MALT1 and MAP3K7 genes in pediatric celiac disease. HUMAN GENE 2023; 36:201180. [DOI: 10.1016/j.humgen.2023.201180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
|
12
|
Nikiphorou E, Philippou E. Nutrition and its role in prevention and management of rheumatoid arthritis. Autoimmun Rev 2023; 22:103333. [PMID: 37182439 DOI: 10.1016/j.autrev.2023.103333] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/13/2023] [Indexed: 05/16/2023]
Abstract
Accumulating research evidence suggests that nutrition might be implicated in the risk of development and in the management of autoimmune disease, including rheumatoid arthritis (RA), characterized by immune-inflammatory response. Nutrition can have direct roles through the provision of pro- or anti-inflammatory foods, and indirect roles through management of co-morbidity management. The review updates on the evidence relating RA risk and management with focus on specific foods such as fish and diets/dietary patterns such as the Mediterranean diet, fasting and elimination diets and oral nutritional supplements including omega-3 polyunsaturated fatty acids (PUFA). Evidence on herbs and spices, beverages, Vitamin D, and probiotics is also reviewed. Diet has been shown to improve disease activity through reducing inflammation and oxidation and through its beneficial effects on the gut microbiota. Based on the existing evidence, it is recommended that as an adjunct to medical treatment, nutrition therapy for RA should be based on an anti-inflammatory Mediterranean diet (MD) supplemented with at least twice a week consumption of oily fish and/or omega-3 PUFA supplements at 2 g/day. The need for rheumatologists to work more closely with registered dietitians in the management of patients particularly in supporting a well-balanced diet according to individual needs, is highlighted.
Collapse
Affiliation(s)
- Elena Nikiphorou
- Department of Rheumatology, King's College Hospital, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK
| | - Elena Philippou
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus; Department of Nutritional Sciences, King's College London, London, UK.
| |
Collapse
|
13
|
Wang NN, Zhang Y, Jiang F, Zhu DL, Di CX, Hu SY, Chen XF, Zhi LQ, Rong Y, Ke X, Duan YY, Dong SS, Yang TL, Yang Z, Guo Y. Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis. Am J Hum Genet 2023; 110:625-637. [PMID: 36924774 PMCID: PMC10119143 DOI: 10.1016/j.ajhg.2023.02.012] [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: 10/19/2022] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Genome-wide association studies (GWASs) have repeatedly reported multiple non-coding single-nucleotide polymorphisms (SNPs) at 2p14 associated with rheumatoid arthritis (RA), but their functional roles in the pathological mechanisms of RA remain to be explored. In this study, we integrated a series of bioinformatics and functional experiments and identified three intronic RA SNPs (rs1876518, rs268131, and rs2576923) within active enhancers that can regulate the expression of SPRED2 directly. At the same time, SPRED2 and ACTR2 influence each other as a positive feedback signal amplifier to strengthen the protective role in RA by inhibiting the migration and invasion of rheumatoid fibroblast-like synoviocytes (FLSs). In particular, the transcription factor CEBPB preferentially binds to the rs1876518-T allele to increase the expression of SPRED2 in FLSs. Our findings decipher the molecular mechanisms behind the GWAS signals at 2p14 for RA and emphasize SPRED2 as a potential candidate gene for RA, providing a potential target and direction for precise treatment of RA.
Collapse
Affiliation(s)
- Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yan Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Chen-Xi Di
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shou-Ye Hu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Li-Qiang Zhi
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Zhi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China.
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.
| |
Collapse
|
14
|
Wu KC, Condon ND, Hill TA, Reid RC, Fairlie DP, Lim J. Ras-Related Protein Rab5a Regulates Complement C5a Receptor Trafficking, Chemotaxis, and Chemokine Secretion in Human Macrophages. J Innate Immun 2023; 15:468-484. [PMID: 36882040 PMCID: PMC10105068 DOI: 10.1159/000530012] [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: 10/12/2022] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Complement activation and Rab GTPase trafficking are commonly observed in inflammatory responses. Recruitment of innate immune cells to sites of infection or injury and secretion of inflammatory chemokines are promoted by complement component 5a (C5a) that activates the cell surface protein C5a receptor1 (C5aR1). Persistent activation can lead to a myriad of inflammatory and autoimmune diseases. Here, we demonstrate that the mechanism of C5a induced chemotaxis of human monocyte-derived macrophages (HMDMs) and their secretion of inflammatory chemokines are controlled by Rab5a. We find that C5a activation of the G protein coupled receptor C5aR1 expressed on the surface of HMDMs, recruits β-arrestin2 via Rab5a trafficking, then activates downstream phosphatidylinositol 3-kinase (PI3K)/Akt signaling that culminates in chemotaxis and secretion of pro-inflammatory chemokines from HMDMs. High-resolution lattice light-sheet microscopy on live cells showed that C5a activates C5aR1-GFP internalization and colocalization with Rab5a-tdTomato but not with dominant negative mutant Rab5a-S34N-tdTomato in HEK293 cells. We found that Rab5a is significantly upregulated in differentiated HMDMs and internalization of C5aR1 is dependent on Rab5a. Interestingly, while knockdown of Rab5a inhibited C5aR1-mediated Akt phosphorylation, it did not affect C5aR1-mediated ERK1/2 phosphorylation or intracellular calcium mobilization in HMDMs. Functional analysis using transwell migration and µ-slide chemotaxis assays indicated that Rab5a regulates C5a-induced chemotaxis of HMDMs. Further, C5aR1 was found to mediate interaction of Rab5a with β-arrestin2 but not with G proteins in HMDMs. Furthermore, C5a-induced secretion of pro-inflammatory chemokines (CCL2, CCL3) from HMDMs was attenuated by Rab5a or β-arrestin2 knockdown or by pharmacological inhibition with a C5aR1 antagonist or a PI3K inhibitor. These findings reveal a C5a-C5aR1-β-arrestin2-Rab5a-PI3K signaling pathway that regulates chemotaxis and pro-inflammatory chemokine secretion in HMDMs and suggests new ways of selectively modulating C5a-induced inflammatory outputs.
Collapse
Affiliation(s)
- Kai-Chen Wu
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nicholas D. Condon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy A. Hill
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Robert C. Reid
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - David P. Fairlie
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Junxian Lim
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
15
|
Innate and adaptive immune abnormalities underlying autoimmune diseases: the genetic connections. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-021-2187-3. [PMID: 36738430 PMCID: PMC9898710 DOI: 10.1007/s11427-021-2187-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/10/2022] [Indexed: 02/05/2023]
Abstract
With the exception of an extremely small number of cases caused by single gene mutations, most autoimmune diseases result from the complex interplay between environmental and genetic factors. In a nutshell, etiology of the common autoimmune disorders is unknown in spite of progress elucidating certain effector cells and molecules responsible for pathologies associated with inflammatory and tissue damage. In recent years, population genetics approaches have greatly enriched our knowledge regarding genetic susceptibility of autoimmunity, providing us with a window of opportunities to comprehensively re-examine autoimmunity-associated genes and possible pathways. In this review, we aim to discuss etiology and pathogenesis of common autoimmune disorders from the perspective of human genetics. An overview of the genetic basis of autoimmunity is followed by 3 chapters detailing susceptibility genes involved in innate immunity, adaptive immunity and inflammatory cell death processes respectively. With such attempts, we hope to expand the scope of thinking and bring attention to lesser appreciated molecules and pathways as important contributors of autoimmunity beyond the 'usual suspects' of a limited subset of validated therapeutic targets.
Collapse
|
16
|
Meng Z, Ma Y, Li W, Deng X. Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study. PeerJ 2023; 11:e14595. [PMID: 36718446 PMCID: PMC9884046 DOI: 10.7717/peerj.14595] [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: 04/29/2022] [Accepted: 11/28/2022] [Indexed: 01/26/2023] Open
Abstract
Background and Objective Epidemiological studies report associations between coronavirus disease 2019 (COVID-19) and periodontitis; however, causality has not been proven. The aim of this study is to assess the associations between COVID-19 susceptibility and periodontitis with two-sample Mendelian randomization (MR) analyses. Methods A two-sample summary MR analysis was performed using data for outcome and exposure from the OpenGWAS database on people of European descent. Periodontal complex traits (PCTs) were chosen as a proxy for the periodontitis phenotype. The causal association between PCT3 (Aggregatibacter actinomycetemcomitans), PCT5 (Porphyromonas gingivalis), and gingival crevicular fluid (GCF) interleukin-1β (IL-1β) and COVID-19 were considered. Genome-wide association study (GWAS) data with the two largest sample sizes were selected as COVID-19 outcomes (datasets ebi-a-GCST010776 and ebi-a-GCST010777). Single-nucleotide polymorphisms (SNPs) associated with PCT3, PCT5, and GCF IL-1β at statistical significance at genome-wide level (P < 5 × 10-8) were identified as genetic instruments. We used two-sample summary MR methods and tested the existence of a pleiotropic effect with MR-Egger. Results Inverse-variance weighted (IVW) estimates showed that there was a positive association between COVID-19 risk and periodontitis (ebi-a-GCST010776: odds ratio [OR] = 1.02 (95% confidence interval (CI), 1.00-1.05), P = 0.0171; ebi-a-GCST010777: OR = 1.03 (95% CI, 1.00-1.05), P = 0.0397). The weighted median also showed directionally similar estimates. Exploration of the causal associations between other PCTs and COVID-19 identified a slight effect of local inflammatory response (GCF IL-1β) on COVID-19 risk across the two datasets (ebi-a-GCST010776: IVW OR = 1.02 (95% CI, [1.01-1.03]), P < 0.001; ebi-a-GCST010777: IVW OR = 1.03 (95% CI, [1.02-1.04]), P < 0.001). The intercepts of MR-Egger yielded no proof for significant directional pleiotropy for either dataset (ebi-a-GCST010776: P = 0.7660; ebi-a-GCST010777: P = 0.6017). Conclusions The findings suggests that periodontitis and the higher GCF IL-1β levels is causally related to increase susceptibility of COVID-19. However, given the limitations of our study, the well-designed randomized controlled trials are needed to confirm its findings, which may represent a new non-pharmaceutical intervention for preventing COVID-19.
Collapse
Affiliation(s)
- Zhaoqiang Meng
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yujia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, P. R. China
| | - Wenjing Li
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China,Peking University Health Science Center, Institute of Medical Technology, Beijing, P. R. China,Key Laboratory of Dental Material, National Medical Products Administration, Beijing, China
| | - Xuliang Deng
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China,Key Laboratory of Dental Material, National Medical Products Administration, Beijing, China
| |
Collapse
|
17
|
Targeting protein phosphatases in cancer immunotherapy and autoimmune disorders. Nat Rev Drug Discov 2023; 22:273-294. [PMID: 36693907 PMCID: PMC9872771 DOI: 10.1038/s41573-022-00618-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 01/25/2023]
Abstract
Protein phosphatases act as key regulators of multiple important cellular processes and are attractive therapeutic targets for various diseases. Although extensive effort has been dedicated to phosphatase-targeted drug discovery, early expeditions for competitive phosphatase inhibitors were plagued by druggability issues, leading to the stigmatization of phosphatases as difficult targets. Despite challenges, persistent efforts have led to the identification of several drug-like, non-competitive modulators of some of these enzymes - including SH2 domain-containing protein tyrosine phosphatase 2, protein tyrosine phosphatase 1B, vascular endothelial protein tyrosine phosphatase and protein phosphatase 1 - reigniting interest in therapeutic targeting of phosphatases. Here, we discuss recent progress in phosphatase drug discovery, with emphasis on the development of selective modulators that exhibit biological activity. The roles and regulation of protein phosphatases in immune cells and their potential as powerful targets for immuno-oncology and autoimmunity indications are assessed.
Collapse
|
18
|
Philippou E, Nikiphorou E. Answer to Cafaro et al. by Philippou E and Nikiphorou E. Joint Bone Spine 2022; 105471. Joint Bone Spine 2023; 90:105474. [PMID: 36471544 DOI: 10.1016/j.jbspin.2022.105474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Elena Philippou
- Department of Life, Health Sciences, School of Sciences, Engineering, University of Nicosia, Nicosia, Cyprus; Department of Nutritional Sciences, King's College London, London, UK
| | - Elena Nikiphorou
- Department of Rheumatology, King's College Hospital, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK.
| |
Collapse
|
19
|
Lal R, Bhardwaj R, Minz RW, Prasad KK, Lal S, Dayal D, Kumar Y. Usefulness of a double immunofluorescence technique for detection of intestinal tTG-IgA deposits in diabetic and non-diabetic children with celiac disease. Pediatr Neonatol 2022:S1875-9572(22)00269-8. [PMID: 36610914 DOI: 10.1016/j.pedneo.2022.01.012] [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: 09/18/2021] [Revised: 12/30/2021] [Accepted: 01/18/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Celiac disease (CD) is frequently associated with type I diabetes mellitus (T1D), where its diagnosis may be a challenging task. This study aims to test the usefulness of the double staining immunofluorescence (dsIF) technique for the detection of intestinal anti-tissue transglutaminase specific IgA antibody (tTG-IgA) deposits in CD and T1D children with coexisting CD. METHODS A total of 46 patients (30 cases of CD and 16 cases of T1D with CD) and 16 non-diabetic, non-celiac children were recruited. Endoscopic biopsies were taken and analyzed by light microscopy, quantitative histology (QH), and a dsIF technique. RESULTS Histologically, villous atrophy was most severe in CD, followed by T1D with CD, while all control biopsies except 1 were normal. QH showed a statistically significant difference in villous height (Vh), crypt depth (CrD), and Vh:CrD ratio between diabetic and non-diabetic patients with CD. dsIF technique could detect tTG-IgA deposits in 85.7% of cases of CD alone and 93.8% of biopsies from diabetic children. Surprisingly, deposits were more extensive in biopsies with minimal villous shortening. Also, all 5 biopsies from T1D patients with normal histology were dsIF positive. CONCLUSION In-situ analysis of tTG-IgA immune deposits facilitates the detection of positive serology early-onset CD. Quantitative analysis may be used as an ancillary tool to increase the reliability of histological findings in these patients.
Collapse
Affiliation(s)
- Raghav Lal
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Ranjeet Bhardwaj
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Ranjana Walker Minz
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Kaushal Kishore Prasad
- Department of Gastroenterology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Sadhna Lal
- Department of Pediatric Gastroenterology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Devi Dayal
- Department of Pediatric Endocrinology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Yashwant Kumar
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India.
| |
Collapse
|
20
|
Risk of Juvenile Idiopathic Arthritis and Rheumatoid Arthritis in Patients With Celiac Disease: A Population-Based Cohort Study. Am J Gastroenterol 2022; 117:1971-1981. [PMID: 36114769 DOI: 10.14309/ajg.0000000000002014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Celiac disease (CD) is associated with many immune-mediated conditions, but a definitive epidemiological association between CD and juvenile idiopathic arthritis (JIA) or rheumatoid arthritis (RA) has not been established. We quantified the risk of JIA and RA among patients with CD using a population-based cohort. METHODS We identified patients diagnosed with biopsy-proven CD between 2004 and 2017 using data from a national histopathology cohort in Sweden. Each patient was matched by age, sex, calendar year, and geographic region to reference individuals in the general population. We calculated the incidence and estimated the relative risk, through Cox proportional hazards models, of JIA in individuals with CD aged <18 and of RA in individuals with CD aged ≥18. RESULTS We identified 24,014 individuals with CD who were matched to 117,397 reference individuals from the general population. Among individuals aged <18, the incidence rate of JIA was 5.9 per 10,000 person-years in patients with CD and 2.2 per 10,000 person-years in the general population (n events = 40 and 73, respectively; hazard ratio [HR] 2.68, 95% confidence interval 1.82-3.95) over a follow-up of 7.0 years. Among individuals aged ≥ 18, the incidence of RA was 8.4 per 10,000 person-years in CD and 5.1 per 10,000 person-years in matched comparators (n events = 110 and 322, respectively; HR 1.70, 95% confidence interval 1.36-2.12) over a follow-up of 8.8 years. DISCUSSION Among children with CD, JIA develops nearly 3 times as often as it does in the general population, and among adults with CD, RA occurs nearly 2 times as often. Clinicians caring for patients with CD with joint symptoms should have a low threshold to evaluate for JIA or RA.
Collapse
|
21
|
Liu S, Gong W, Liu L, Yan R, Wang S, Yuan Z. Integrative Analysis of Transcriptome-Wide Association Study and Gene-Based Association Analysis Identifies In Silico Candidate Genes Associated with Juvenile Idiopathic Arthritis. Int J Mol Sci 2022; 23:13555. [PMID: 36362342 PMCID: PMC9656154 DOI: 10.3390/ijms232113555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 07/02/2024] Open
Abstract
Genome-wide association study (GWAS) of Juvenile idiopathic arthritis (JIA) suffers from low power due to limited sample size and the interpretation challenge due to most signals located in non-coding regions. Gene-level analysis could alleviate these issues. Using GWAS summary statistics, we performed two typical gene-level analysis of JIA, transcriptome-wide association studies (TWAS) using FUnctional Summary-based ImputatiON (FUSION) and gene-based analysis using eQTL Multi-marker Analysis of GenoMic Annotation (eMAGMA), followed by comprehensive enrichment analysis. Among 33 overlapped significant genes from these two methods, 11 were previously reported, including TYK2 (PFUSION = 5.12 × 10-6, PeMAGMA = 1.94 × 10-7 for whole blood), IL-6R (PFUSION = 8.63 × 10-7, PeMAGMA = 2.74 × 10-6 for cells EBV-transformed lymphocytes), and Fas (PFUSION = 5.21 × 10-5, PeMAGMA = 1.08 × 10-6 for muscle skeletal). Some newly plausible JIA-associated genes are also reported, including IL-27 (PFUSION = 2.10 × 10-7, PeMAGMA = 3.93 × 10-8 for Liver), LAT (PFUSION = 1.53 × 10-4, PeMAGMA = 4.62 × 10-7 for Artery Aorta), and MAGI3 (PFUSION = 1.30 × 10-5, PeMAGMA = 1.73 × 10-7 for Muscle Skeletal). Enrichment analysis further highlighted 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 10 Gene Ontology (GO) terms. Our findings can benefit the understanding of genetic determinants and potential therapeutic targets for JIA.
Collapse
Affiliation(s)
- Shuai Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Weiming Gong
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Lu Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Ran Yan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shukang Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| |
Collapse
|
22
|
Philippou E, Nikiphorou E. Gluten or no gluten for rheumatic diseases? Joint Bone Spine 2022; 89:105453. [PMID: 35964884 DOI: 10.1016/j.jbspin.2022.105453] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Elena Philippou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus; Department of Nutritional Sciences, King's College London, London, UK.
| | - Elena Nikiphorou
- Department of Rheumatology, King's College Hospital, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK.
| |
Collapse
|
23
|
Hua L, Xiang S, Xu R, Xu X, Liu T, Shi Y, Wu L, Wang R, Sun Q. Causal association between rheumatoid arthritis and celiac disease: A bidirectional two-sample mendelian randomization study. Front Genet 2022; 13:976579. [PMID: 36330450 PMCID: PMC9623103 DOI: 10.3389/fgene.2022.976579] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/06/2022] [Indexed: 01/23/2024] Open
Abstract
Objectives: Rheumatoid Arthritis (RA) has been associated with Celiac Disease (CD) in previous observational epidemiological studies. However, evidence for this association is limited and inconsistent, and it remains uncertain whether the association is causal or due to confounding or reverse causality. This study aimed to assess the bidirectional causal relationship between RA and CD. Methods: In this two-sample Mendelian randomization (MR) study, instrumental variables (IVs) for RA were derived from a genome-wide association studies (GWAS) meta-analysis including 58,284 subjects. Summary statistics for CD originated from a GWAS meta-analysis with 15,283 subjects. The inverse-variance weighted (IVW) method was used as the primary analysis. Four complementary methods were applied, including the weighted-median, weighted mode, MR pleiotropy residual sum and outlier (MR-PRESSO) test and MR-Egger regression, to strengthen the effect estimates. Results: Positive causal effects of genetically increased RA risk on CD were derived [IVW odds ratio (OR): 1.46, 95% confidence interval (CI): 1.19-1.79, p = 3.21E-04]. The results of reverse MR analysis demonstrated no significant causal effect of CD on RA (IVW OR: 1.05, 95% CI: 0.91-1.21, p = 0.499). According to the sensitivity analysis, horizontal pleiotropy was unlikely to distort the causal estimates. Conclusion: This study reveals a causality of RA on CD but not CD on RA among patients of European descent. This outcome suggests that the features and indicators of CD should regularly be assessed for RA patients.
Collapse
Affiliation(s)
- Lijiangshan Hua
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shate Xiang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Rixiang Xu
- School of Humanities and Management, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Xiao Xu
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Ting Liu
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yanan Shi
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lingyun Wu
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Rongyun Wang
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Qiuhua Sun
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| |
Collapse
|
24
|
Zubkiewicz-Kucharska A, Jamer T, Chrzanowska J, Akutko K, Pytrus T, Stawarski A, Noczyńska A. Prevalence of haplotype DQ2/DQ8 and celiac disease in children with type 1 diabetes. Diabetol Metab Syndr 2022; 14:128. [PMID: 36096955 PMCID: PMC9465882 DOI: 10.1186/s13098-022-00897-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
UNLABELLED Type 1 diabetes (T1D) and celiac disease (CD) coexist very often. Identification of the human leukocyte antigen (HLA) DQ2/DQ8 can confirm the genetic predisposition to CD. Negative result of this test allows to exclude CD with a high probability. It was suggested that in individuals with higher risk of CD, including T1D patients, the implementation of genetic testing should reduce the number of patients requiring systematic immunological screening. The aim of this study was to analyze the prevalence of different haplotypes predisposing to CD in children and adolescents with previously diagnosed T1D. MATERIAL AND METHODS A retrospective analysis was performed on 166 T1D children (91 girls) in whom HLA DQ2/DQ8 alleles were tested. In 9.6% CD was also diagnosed. RESULTS In 12.7% both HLA DQ2/DQ8 were negative. In 87.3% patients HLA DQ2 and/or DQ8 was positive, including 27.7% patients with both haplotypes DQ2.5 and DQ8 positive. In all CD patients the disease predisposing alleles were positive, while none of the HLA DQ2/DQ8 negative children were diagnosed with CD. CONCLUSIONS The prevalence of HLA DQ2.5 and the HLA DQ2.5 / HLA DQ8 configuration is higher in patients with T1D, and CD compared to children with T1D alone. The combination of HLA DQ2 and HLA DQ8 most significantly increases the risk of developing CD. The group of HLA DQ2/DQ8 negative patients with improbable CD diagnosis, is relatively small. Most of T1D patients HLA DQ2/DQ8 positive need further regular antibody assessment. In patients with T1D, who are at high risk of developing CD, genetic testing may be considered to select those who require further systematic serological evaluation. Due to its retrospective nature, the study was not registered in the database of clinical trials and the Clinical trial registration number is not available.
Collapse
Affiliation(s)
- Agnieszka Zubkiewicz-Kucharska
- Department of Pediatric Endocrinology and Diabetology for Children and Adolescents, Wroclaw Medical University, Wroclaw, Poland
| | - Tatiana Jamer
- Department of Pediatrics, Gastroenterology and Nutrition, Wroclaw Medical University, Wroclaw, Poland.
| | - Joanna Chrzanowska
- Department of Pediatric Endocrinology and Diabetology for Children and Adolescents, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Akutko
- Department of Pediatrics, Gastroenterology and Nutrition, Wroclaw Medical University, Wroclaw, Poland
| | - Tomasz Pytrus
- Department of Pediatrics, Gastroenterology and Nutrition, Wroclaw Medical University, Wroclaw, Poland
| | - Andrzej Stawarski
- Department of Pediatrics, Gastroenterology and Nutrition, Wroclaw Medical University, Wroclaw, Poland
| | - Anna Noczyńska
- Department of Pediatric Endocrinology and Diabetology for Children and Adolescents, Wroclaw Medical University, Wroclaw, Poland
| |
Collapse
|
25
|
Khunsriraksakul C, Markus H, Olsen NJ, Carrel L, Jiang B, Liu DJ. Construction and Application of Polygenic Risk Scores in Autoimmune Diseases. Front Immunol 2022; 13:889296. [PMID: 35833142 PMCID: PMC9271862 DOI: 10.3389/fimmu.2022.889296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with autoimmune diseases and provided unique mechanistic insights and informed novel treatments. These individual genetic variants on their own typically confer a small effect of disease risk with limited predictive power; however, when aggregated (e.g., via polygenic risk score method), they could provide meaningful risk predictions for a myriad of diseases. In this review, we describe the recent advances in GWAS for autoimmune diseases and the practical application of this knowledge to predict an individual’s susceptibility/severity for autoimmune diseases such as systemic lupus erythematosus (SLE) via the polygenic risk score method. We provide an overview of methods for deriving different polygenic risk scores and discuss the strategies to integrate additional information from correlated traits and diverse ancestries. We further advocate for the need to integrate clinical features (e.g., anti-nuclear antibody status) with genetic profiling to better identify patients at high risk of disease susceptibility/severity even before clinical signs or symptoms develop. We conclude by discussing future challenges and opportunities of applying polygenic risk score methods in clinical care.
Collapse
Affiliation(s)
- Chachrit Khunsriraksakul
- Graduate Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Havell Markus
- Graduate Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Nancy J. Olsen
- Department of Medicine, Division of Rheumatology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Bibo Jiang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Dajiang J. Liu
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, United States
- *Correspondence: Dajiang J. Liu,
| |
Collapse
|
26
|
Celdir MG, Jansson-Knodell CL, Hujoel IA, Prokop LJ, Wang Z, Murad MH, Murray JA. Latitude and Celiac Disease Prevalence: A Meta-Analysis and Meta-Regression. Clin Gastroenterol Hepatol 2022; 20:e1231-e1239. [PMID: 33007509 DOI: 10.1016/j.cgh.2020.09.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/15/2020] [Accepted: 09/20/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The latitudinal gradient effect is described for several autoimmune diseases including celiac disease in the United States. However, the association between latitude and global celiac disease prevalence is unknown. We aimed to explore the association between latitude and serology-based celiac disease prevalence through meta-analysis. METHODS We searched MEDLINE, Embase, Cochrane, and Scopus databases from their beginning through June 29, 2018, to identify screening studies that targeted a general population sample, used serology-based screening tests, and provided a clear location from which we could assign a latitude. Studies were excluded if sampling was based on symptoms, risk factors, or referral. Study selection and data extraction were performed by independent reviewers. The association measures between latitude and prevalence of serology-based celiac disease were evaluated with random-effects meta-analyses and meta-regression. RESULTS Of the identified 4667 unique citations, 128 studies were included, with 155 prevalence estimates representing 40 countries. Celiac disease was more prevalent at the higher latitudes of 51° to 60° (relative risk [RR], 1.62; 95% CI, 1.09-2.38) and 61° to 70° (RR, 2.30; 95% CI, 1.36-3.89) compared with the 41° to 50° reference level. No statistically significant difference was observed at lower latitudes. When latitude was treated as continuous, we found a statistically significant association between CD prevalence and latitude overall in the world (RR, 1.03, 95% CI, 1.01-1.05) and a subregional analysis of Europe (RR, 1.05; 95% CI, 1.02-1.07) and North America (RR, 1.1; 95% CI, 1.0-1.2). CONCLUSIONS In this comprehensive review of screening studies, we found that a higher latitude was associated with greater serology-based celiac disease prevalence.
Collapse
Affiliation(s)
- Melis G Celdir
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Isabel A Hujoel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Zhen Wang
- Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, Minnesota
| | - M Hassan Murad
- Robert D. and Patricia E. Kern Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, Minnesota
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
27
|
Zhang X, Huo C, Liu Y, Su R, Zhao Y, Li Y. Mechanism and Disease Association With a Ubiquitin Conjugating E2 Enzyme: UBE2L3. Front Immunol 2022; 13:793610. [PMID: 35265070 PMCID: PMC8899012 DOI: 10.3389/fimmu.2022.793610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Ubiquitin conjugating enzyme E2 is an important component of the post-translational protein ubiquitination pathway, which mediates the transfer of activated ubiquitin to substrate proteins. UBE2L3, also called UBcH7, is one of many E2 ubiquitin conjugating enzymes that participate in the ubiquitination of many substrate proteins and regulate many signaling pathways, such as the NF-κB, GSK3β/p65, and DSB repair pathways. Studies on UBE2L3 have found that it has an abnormal expression in many diseases, mainly immune diseases, tumors and Parkinson’s disease. It can also promote the occurrence and development of these diseases. Resultantly, UBE2L3 may become an important target for some diseases. Herein, we review the structure of UBE2L3, and its mechanism in diseases, as well as diseases related to UBE2L3 and discuss the related challenges.
Collapse
Affiliation(s)
- Xiaoxia Zhang
- Department of Ophthalmology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Chengdong Huo
- Department of Ophthalmology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yating Liu
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Ruiliang Su
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yang Zhao
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Yumin Li
- Key Laboratory of the Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| |
Collapse
|
28
|
Sandhu G, Thelma BK. New Druggable Targets for Rheumatoid Arthritis Based on Insights From Synovial Biology. Front Immunol 2022; 13:834247. [PMID: 35265082 PMCID: PMC8899708 DOI: 10.3389/fimmu.2022.834247] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 12/19/2022] Open
Abstract
Rheumatoid arthritis (RA) is a multifactorial autoimmune disease characterized by chronic inflammation and destruction of multiple small joints which may lead to systemic complications. Altered immunity via pathogenic autoantibodies pre-date clinical symptom development by several years. Incompletely understood range of mechanisms trigger joint-homing, leading to clinically evident articular disease. Advances in therapeutic approaches and understanding pathogenesis have improved prognosis and likely remission. However, partial/non-response to conventional and biologic therapies witnessed in a subset of patients highlights the need for new therapeutics. It is now evident that joint disease chronicity stems from recalcitrant inflammatory synovial environment, majorly maintained by epigenetically and metabolically reprogrammed synoviocytes. Therefore, interference with effector functions of activated cell types seems a rational strategy to reinstate synovial homeostasis and complement existing anti-inflammatory interventions to mitigate chronic RA. Presenting this newer aspect of fibroblast-like synoviocytes and myeloid cells underlying the altered synovial biology in RA and its potential for identification of new druggable targets is attempted in this review. Major leads from i) molecular insights of pathogenic cell types from hypothesis free OMICS approaches; ii) hierarchy of their dysregulated signaling pathways; and iii) knowledge of druggability of molecular nodes in these pathways are highlighted. Development of such synovial biology-directed therapeutics hold promise for an enriched drug repertoire for RA.
Collapse
Affiliation(s)
| | - B. K. Thelma
- Department of Genetics, University of Delhi, New Delhi, India
| |
Collapse
|
29
|
Fang YD, Zhao J, Zhuang XJ, Xu JB, Cai TT, Yang XR, Mu KD, Zhang JA. Association of ANKRD55 Gene Polymorphism with HT: A Protective Factor for Disease Susceptibility. Int J Endocrinol 2022; 2022:7300796. [PMID: 35983018 PMCID: PMC9381225 DOI: 10.1155/2022/7300796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
PURPOSE Recent studies have shown that Ankyrin Repeat Domain 55 (ANKRD55) gene polymorphism is a risk factor for multiple autoimmune diseases, but its association with autoimmune thyroid diseases (AITDs) has not been reported. The purpose of this study was to investigate the potential relationship between polymorphism of the ANKRD55 gene and AITDs. METHODS For this study, we enrolled 2050 subjects, consisting of 1220 patients with AITD and 830 healthy subjects. Five loci (rs321776, rs191205, rs7731626, rs415407, and rs159572) of the ANKRD55 gene were genotyped using Multiplex PCR combined with high-throughput sequencing. RESULTS The results showed that the allele frequencies of rs7731626 and rs159572 loci in HT patients were lower than those in normal controls (P=0.048 and P=0.03, respectively). In different genetic model analyses, rs7731626 and rs159572 were also significantly correlated with HT in allele, dominant and additive models before and after age and sex adjustment. There were no differences in rs321776, rs191205, or rs415407 of the ANKRD55 gene in allele frequency or genotype frequency between AITDs patients and controls. CONCLUSIONS This study for the first time found that rs7731626 and rs159572 of ANKRD55 were significantly correlated with HT, and individuals carrying the A allele at these two loci had a lower probability of developing HT.
Collapse
Affiliation(s)
- Yu-die Fang
- Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jing Zhao
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Xin-juan Zhuang
- Department of Endocrinology, Jinshan Branch of Shanghai Sixth People's Hospital, Shanghai 201318, China
| | - Jian-bin Xu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Tian-tian Cai
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Xiao-rong Yang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Kai-da Mu
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
| | - Jin-an Zhang
- Department of Endocrinology & Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201599, China
- Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| |
Collapse
|
30
|
Xie Y, Li M, Dong W, Jiang W, Zhao H. M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits. PLoS Genet 2021; 17:e1009849. [PMID: 34735430 PMCID: PMC8568192 DOI: 10.1371/journal.pgen.1009849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022] Open
Abstract
Recent studies have demonstrated that multiple early-onset diseases have shared risk genes, based on findings from de novo mutations (DNMs). Therefore, we may leverage information from one trait to improve statistical power to identify genes for another trait. However, there are few methods that can jointly analyze DNMs from multiple traits. In this study, we develop a framework called M-DATA (Multi-trait framework for De novo mutation Association Test with Annotations) to increase the statistical power of association analysis by integrating data from multiple correlated traits and their functional annotations. Using the number of DNMs from multiple diseases, we develop a method based on an Expectation-Maximization algorithm to both infer the degree of association between two diseases as well as to estimate the gene association probability for each disease. We apply our method to a case study of jointly analyzing data from congenital heart disease (CHD) and autism. Our method was able to identify 23 genes for CHD from joint analysis, including 12 novel genes, which is substantially more than single-trait analysis, leading to novel insights into CHD disease etiology.
Collapse
Affiliation(s)
- Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mo Li
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Wei Jiang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| |
Collapse
|
31
|
Li Y, Xiao FL, Cheng H, Liang B, Zhou FS, Li P, Zheng XD, Sun LD, Yang S, Zhang XJ. A Common Variant at 11q23.3 Is Associated with Susceptibility to Atopic Dermatitis in the Han Chinese Population. Genet Test Mol Biomarkers 2021; 25:638-645. [PMID: 34609929 DOI: 10.1089/gtmb.2020.0335] [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: 11/13/2022] Open
Abstract
Background: Genome-wide association studies (GWASs) have identified many genetic variants that are risk factors for numerous immune-mediated diseases. In particular, different immune-mediated diseases have been found to share the same susceptibility loci. Therefore, exploring the genetic overlap between atopic dermatitis (AD) and other immune-mediated diseases in more detail may help identify additional shared susceptibility loci among common immune-mediated diseases. Recent evidence suggests that the 11q23.3 locus is a susceptibility locus shared among multiple immune-mediated diseases. Objective: This study was designed to investigated whether SNPs at the chromosome 11q23.3 locus are associated with AD in the Han Chinese population. Methods: In total, 16 SNPs within the 11q23.3 locus were genotyped using TaqMan assays for 1,012 AD cases and 1,362 controls. From these SNPs, we selected rs638893 with an association values of p < 5 × 10-2 for AD for further analysis in an independent replication study using the Sequenom MassARRAY system to genotype an additional (consisting of 1,288 cases and 1,380 controls). The combined analyses were performed in two stages using a meta-analytical method. Results: We identified a common variant at 11q23.3 (rs638893), that was significantly associated (p = 1.58 × 10-3, OR = 1.22) with AD. The genotype-based association analysis revealed that the recessive model provided the best fit for rs638893. Conclusion: Our study identified a variant on chromosome 11q23.3 that likely confers susceptibility to AD, thereby advancing our understanding of the genetic basis of this disease.
Collapse
Affiliation(s)
- Yang Li
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Feng-Li Xiao
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Hui Cheng
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Bo Liang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Fu-Sheng Zhou
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Pan Li
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Xiao-Dong Zheng
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Liang-Dan Sun
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Sen Yang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| | - Xue-Jun Zhang
- Department of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China
| |
Collapse
|
32
|
Gupta VK, Cunningham KY, Hur B, Bakshi U, Huang H, Warrington KJ, Taneja V, Myasoedova E, Davis JM, Sung J. Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis. Genome Med 2021; 13:149. [PMID: 34517888 PMCID: PMC8439035 DOI: 10.1186/s13073-021-00957-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Rapid advances in the past decade have shown that dysbiosis of the gut microbiome is a key hallmark of rheumatoid arthritis (RA). Yet, the relationship between the gut microbiome and clinical improvement in RA disease activity remains unclear. In this study, we explored the gut microbiome of patients with RA to identify features that are associated with, as well as predictive of, minimum clinically important improvement (MCII) in disease activity. METHODS We conducted a retrospective, observational cohort study on patients diagnosed with RA between 1988 and 2014. Whole metagenome shotgun sequencing was performed on 64 stool samples, which were collected from 32 patients with RA at two separate time-points approximately 6-12 months apart. The Clinical Disease Activity Index (CDAI) of each patient was measured at both time-points to assess achievement of MCII; depending on this clinical status, patients were distinguished into two groups: MCII+ (who achieved MCII; n = 12) and MCII- (who did not achieve MCII; n = 20). Multiple linear regression models were used to identify microbial taxa and biochemical pathways associated with MCII while controlling for potentially confounding factors. Lastly, a deep-learning neural network was trained upon gut microbiome, clinical, and demographic data at baseline to classify patients according to MCII status, thereby enabling the prediction of whether a patient will achieve MCII at follow-up. RESULTS We found age to be the largest determinant of the overall compositional variance in the gut microbiome (R2 = 7.7%, P = 0.001, PERMANOVA). Interestingly, the next factor identified to explain the most variance in the gut microbiome was MCII status (R2 = 3.8%, P = 0.005). Additionally, by looking at patients' baseline gut microbiome profiles, we observed significantly different microbiome traits between patients who eventually showed MCII and those who did not. Taxonomic features include alpha- and beta-diversity measures, as well as several microbial taxa, such as Coprococcus, Bilophila sp. 4_1_30, and Eubacterium sp. 3_1_31. Notably, patients who achieved clinical improvement had higher alpha-diversity in their gut microbiomes at both baseline and follow-up visits. Functional profiling identified fifteen biochemical pathways, most of which were involved in the biosynthesis of L-arginine, L-methionine, and tetrahydrofolate, to be differentially abundant between the MCII patient groups. Moreover, MCII+ and MCII- groups showed significantly different fold-changes (from baseline to follow-up) in eight microbial taxa and in seven biochemical pathways. These results could suggest that, depending on the clinical course, gut microbiomes not only start at different ecological states, but also are on separate trajectories. Finally, the neural network proved to be highly effective in predicting which patients will achieve MCII (balanced accuracy = 90.0%, leave-one-out cross-validation), demonstrating potential clinical utility of gut microbiome profiles. CONCLUSIONS Our findings confirm the presence of taxonomic and functional signatures of the gut microbiome associated with MCII in RA patients. Ultimately, modifying the gut microbiome to enhance clinical outcome may hold promise as a future treatment for RA.
Collapse
Affiliation(s)
- Vinod K Gupta
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Surgery Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Kevin Y Cunningham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Hur
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Surgery Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Utpal Bakshi
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Surgery Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Harvey Huang
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, USA
| | - Kenneth J Warrington
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Elena Myasoedova
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Health Sciences Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - John M Davis
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jaeyun Sung
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Division of Surgery Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA.
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
33
|
Al-Akioui-Sanz K, Moraru M, Vilches C. A simple genotyping method for CD247 3'-untranslated region polymorphism rs1052231 and characterization of a reference cell panel. HLA 2021; 98:218-222. [PMID: 34233083 PMCID: PMC9291556 DOI: 10.1111/tan.14361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/17/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
CD247 (or CD3‐ζ chain) is an essential adaptor and signal‐transducing molecule of the T‐cell antigen receptor (TCR) complex, and it also couples to NK‐cell activating receptors such as NKp46, NKp30 and CD16A (FcγRIII). Noncoding sequence polymorphisms and variations in CD247 expression, a tightly regulated process, have been related with an altered immune response in multiple health conditions. A single nucleotide polymorphism (T > A) at nucleotide 844 of the CD247 3′‐untranslated region, rs1052231, has been related with lower CD247 gene expression and it has been investigated as a potential biomarker of autoimmune disease. We present here a simple, accurate, reliable, time‐efficient, and cost‐effective method for CD247‐rs1052231 genotyping. Using this method, based on polymerase chain reaction with confronting two‐pair primers (PCR‐CTPP), we have also characterized the CD247‐rs1052231 genotypes in a panel of worldwide available cell lines, which should facilitate study of the role of this polymorphism in immunity and human health.
Collapse
Affiliation(s)
- Karima Al-Akioui-Sanz
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
| | - Manuela Moraru
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
| | - Carlos Vilches
- Immunogenetics & Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Majadahonda, Madrid, Spain
| |
Collapse
|
34
|
Liu YQ, Liu Y, Zhang Q, Xiao T, Deng HW. Identification of Novel Pleiotropic SNPs Associated with Osteoporosis and Rheumatoid Arthritis. Calcif Tissue Int 2021; 109:17-31. [PMID: 33740106 PMCID: PMC8238865 DOI: 10.1007/s00223-021-00817-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/28/2021] [Indexed: 01/21/2023]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of genetic loci for osteoporosis (OP) and rheumatoid arthritis (RA), individually, however, a large proportion of the total trait heritability remains unexplained. Previous studies demonstrated that these two diseases may share some common genetic determination and risk factors, but they were generally focused on individual trait and failed to identify the common variants that play key functional roles in the etiology of these two diseases. Here, we performed a conditional false discovery rate (cFDR) analysis to identify novel pleiotropic variants shared between them by integrating two independent GWASs with summary statistics for total body bone mineral density (TB-BMD, a major risk factor for osteoporosis) (n = 66,628) and RA (n = 58,284). A fine-mapping approach was also applied to identify the most probable causal variants with biological effects on both TB-BMD and RA. As a result, we found 47 independent pleiotropic SNPs shared between TB-BMD and RA, and 40 of them were validated in heel ultrasound estimated BMD (eBMD), femoral neck BMD (FN-BMD) or lumbar spine (LS-BMD). We detected one SNP (rs13299616) was novel and not identified by previous BMD or RA-related studies. Combined with fine-mapping and GWAS-eQTL colocalization analyses, our results suggested that locus 1p13.2 (including PTPN22, MAGI3, PHTF1, and RSBN1) was an important region to regulate TB-BMD and RA simultaneously. These findings provide new insights into the shared biological mechanisms and functional genetic determinants between OP and RA, and novel potential targets for treatment development.
Collapse
Affiliation(s)
- Ying-Qi Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Yong Liu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Qiang Zhang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Tao Xiao
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, 1440 Canal St., Suite 2001, New Orleans, 70112, USA.
| |
Collapse
|
35
|
Saraeva R, Kamenarska Z, Dourmishev L, Vinkov A, Dzhebir G, Kachakova D, Ivanova N, Pozharashka J, Kaneva R, Hristova M. CD3Z polymorphisms and promoter hypermethylation in dermatomyositis - the role of cytosine-phosphate-guanine-related single nucleotide polymorphisms. Immunol Invest 2021; 51:817-825. [PMID: 33902375 DOI: 10.1080/08820139.2021.1876724] [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: 09/30/2022]
Abstract
Background: Decreased expression of the T cell receptor (TCR) ζ-chain has been reported in autoimmune diseases. Recent evidence suggests that this deficiency may be due to polymorphisms in the CD3Z (CD247) gene and/or due to promoter hypermethylation.Methods: Altogether 131 subjects - 36 with dermatomyositis (DM) and 95 healthy controls were genotyped for rs1052230 G > C and rs1052231 T > A polymorphisms using TaqMan assay. The rs840015 G > A polymorphism was analyzed by direct sequencing. The promoter methylation status was analyzed by Sanger sequencing of bisulfite converted DNA.Results: The rs1052230GC genotype and C allele and the rs1052231TA genotype and T allele were found to correlate with photosensitivity as well as the rs1052230C/rs1052231T haplotype. The rs1052231TA genotype was found to be associated with cutaneous disease. The rs840015GG genotype was found increased among patients with DM, leading to increased OR 2.4. On the contrary, the rs840015GA genotype appeared to be protective for the development of DM. From the 11 cytosine-phosphate-guanine (CpG) islands analyzed, only the 8th island showed a difference in its methylation due to the polymorphism rs840015 G > A within this island, as our results suggest. In this way the presence of AA genotype led to no methylation and the presence of the GG genotype was associated with hemimethylation.Conclusion: The CD247 rs1052230 G > C and rs1052231 T > A polymorphisms appeared to have a disease-modifying role. The rs840015GA genotype being associated with reduced methylation has a protective role for the development of dermatomyositis and our results suggest that CpG related single nucleotide polymorphisms may play an important role in autoimmunity.
Collapse
Affiliation(s)
- Radoslava Saraeva
- Medical University Sofia, Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Sofia, Bulgaria
| | - Zornitsa Kamenarska
- Medical University Sofia, Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Sofia, Bulgaria
| | - Lyubomir Dourmishev
- Medical University Sofia, Department of Dermatology and Venereology, University Hospital Alexandrovska, Clinic of Dermatology and Venereology, Sofia, Bulgaria
| | - Anton Vinkov
- Department of Neurology, Hôpitaux Drôme Nord, Romans-sur-Isère, France
| | - Gyulnas Dzhebir
- Medical University Sofia, Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Sofia, Bulgaria
| | - Darina Kachakova
- Medical University Sofia, Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Sofia, Bulgaria
| | - Neviana Ivanova
- Medical University Sofia, Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Sofia, Bulgaria
| | - Joana Pozharashka
- Medical University Sofia, Department of Dermatology and Venereology, University Hospital Alexandrovska, Clinic of Dermatology and Venereology, Sofia, Bulgaria
| | - Radka Kaneva
- Medical University Sofia, Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Sofia, Bulgaria
| | - Maria Hristova
- Department of Internal Medicine, University Hospital St. Ivan Rilski, Clinic of Nephrology, Sofia, Bulgaria
| |
Collapse
|
36
|
van der Graaf A, Zorro MM, Claringbould A, Võsa U, Aguirre-Gamboa R, Li C, Mooiweer J, Ricaño-Ponce I, Borek Z, Koning F, Kooy-Winkelaar Y, Sollid LM, Qiao SW, Kumar V, Li Y, Franke L, Withoff S, Wijmenga C, Sanna S, Jonkers I. Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Disease. Front Genet 2021; 11:562434. [PMID: 33569077 PMCID: PMC7868554 DOI: 10.3389/fgene.2020.562434] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by gluten. Although genome-wide association studies have identified numerous genomic regions associated with CeD, it is difficult to accurately pinpoint which genes in these loci are most likely to cause CeD. We used four different in silico approaches-Mendelian randomization inverse variance weighting, COLOC, LD overlap, and DEPICT-to integrate information gathered from a large transcriptomics dataset. This identified 118 prioritized genes across 50 CeD-associated regions. Co-expression and pathway analysis of these genes indicated an association with adaptive and innate cytokine signaling and T cell activation pathways. Fifty-one of these genes are targets of known drug compounds or likely druggable genes, suggesting that our methods can be used to pinpoint potential therapeutic targets. In addition, we detected 172 gene combinations that were affected by our CeD-prioritized genes in trans. Notably, 41 of these trans-mediated genes appear to be under control of one master regulator, TRAF-type zinc finger domain containing 1 (TRAFD1), and were found to be involved in interferon (IFN)γ signaling and MHC I antigen processing/presentation. Finally, we performed in vitro experiments in a human monocytic cell line that validated the role of TRAFD1 as an immune regulator acting in trans. Our strategy confirmed the role of adaptive immunity in CeD and revealed a genetic link between CeD and IFNγ signaling as well as with MHC I antigen processing, both major players of immune activation and CeD pathogenesis.
Collapse
Affiliation(s)
- Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maria M. Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Raúl Aguirre-Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Chan Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Joram Mooiweer
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Zuzanna Borek
- Deutsches Rheumaforschungszentrum Berlin (DRFZ), An Institute of the Leibniz Association, Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gastroenterology, Infectious Diseases and Rheumatology, Berlin, Germany
| | - Frits Koning
- Department of Immunology, Leiden University, Leiden, Netherlands
| | | | - Ludvig M. Sollid
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hanover, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Istituto di Ricerca Genetica e Biomedica (IRGB) del Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Iris Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | | |
Collapse
|
37
|
Sallese M, Lopetuso LR, Efthymakis K, Neri M. Beyond the HLA Genes in Gluten-Related Disorders. Front Nutr 2020; 7:575844. [PMID: 33262997 PMCID: PMC7688450 DOI: 10.3389/fnut.2020.575844] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Most common food grains contain gluten proteins and can cause adverse medical conditions generally known as gluten-related disorders. Celiac disease is an immune-mediated enteropathy triggered by gluten in individuals carrying a specific genetic make-up. The presence of the human leukocyte antigens (HLA)-DQ2 and HLA-DQ8 haplotypes together with gluten intake is a necessary, although not sufficient, condition, to develop celiac disease. Fine mapping of the human genome has revealed numerous genetic variants important in the development of this disease. Most of the genetic variants are small nucleotide polymorphisms located within promoters and transcriptional enhancer sequences. Their importance is underlined by an increased risk in DQ2/DQ8 carriers who also have these non-HLA alleles. In addition, several immune-mediated diseases share susceptibility loci with celiac disease, shedding light on the reasons for co-occurrence between these diseases. Finally, most of the genes potentially involved in celiac disease by fine genetic mapping of non-HLA loci were confirmed in gene expression studies. In contrast to celiac disease, very little is known about the genetic make-up of non-celiac wheat sensitivity (NCWS), a clinically defined pathology that shares symptoms and gluten dependence with the celiac disease. We recently identified differentially expressed genes and miRNAs in the intestinal mucosa of these patients. Remarkably, the differentially expressed genes were long non-coding RNAs possibly involved in the regulation of cell functions. Thus, we can speculate that important aspects of these diseases depend on alteration of regulatory genetic circuits. Furthermore, our finding suggests that innate immune response is involved in the pathogenic mechanism of NCWS. This review is intended to convey the idea that in order to fully understand celiac disease and its relationship with other gluten-related disorders, it is worth learning more about non-HLA variants.
Collapse
Affiliation(s)
- Michele Sallese
- Department of Medical, Oral and Biotechnological Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Loris Riccardo Lopetuso
- Center for Advanced Studies and Technology (CAST), 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Konstantinos Efthymakis
- Department of Medicine and Aging Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Matteo Neri
- Center for Advanced Studies and Technology (CAST), 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Sciences, 'G. D'Annunzio' University of Chieti-Pescara, Chieti, Italy
| |
Collapse
|
38
|
García-Santisteban I, Romero-Garmendia I, Cilleros-Portet A, Bilbao JR, Fernandez-Jimenez N. Celiac disease susceptibility: The genome and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 358:1-45. [PMID: 33707051 DOI: 10.1016/bs.ircmb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Celiac Disease (CeD) is an immune-mediated complex disease that is triggered by the ingestion of gluten and develops in genetically susceptible individuals. It has been known for a long time that the Human Leucocyte Antigen (HLA) molecules DQ2 and DQ8 are necessary, although not sufficient, for the disease development, and therefore other susceptibility genes and (epi)genetic events must participate in CeD pathogenesis. The advances in Genomics during the last 15 years have made CeD one of the immune-related disorders with the best-characterized genetic component. In the present work, we will first review the main Genome-Wide Association Studies (GWAS) carried out in the disorder, and emphasize post-GWAS discoveries, including diverse integrative strategies, SNP prioritization approaches, and insights into the Microbiome through the host Genomics. Second, we will explore CeD-related Epigenetics and Epigenomics, mostly focusing on the emerging knowledge of the celiac methylome, and the vast but yet under-explored non-coding RNA (ncRNA) landscape. We conclude that much has been done in the field although there are still completely unvisited areas in the post-Genomics of CeD. Chromatin conformation and accessibility, and Epitranscriptomics are promising domains that need to be unveiled to complete the big picture of the celiac Genome.
Collapse
Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain; Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders, CIBERDEM, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain.
| |
Collapse
|
39
|
Ding J, Frantzeskos A, Orozco G. Functional genomics in autoimmune diseases. Hum Mol Genet 2020; 29:R59-R65. [PMID: 32420598 PMCID: PMC7530520 DOI: 10.1093/hmg/ddaa097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
Associations between genetic loci and increased susceptibility to autoimmune disease have been well characterized, however, translating this knowledge into mechanistic insight and patient benefit remains a challenge. While improvements in the precision, completeness and accuracy of our genetic understanding of autoimmune diseases will undoubtedly be helpful, meeting this challenge will require two interlinked problems to be addressed: first which of the highly correlated variants at an individual locus is responsible for increased disease risk, and second what are the downstream effects of this variant. Given that the majority of loci are thought to affect non-coding regulatory elements, the second question is often reframed as what are the target gene(s) and pathways affected by causal variants. Currently, these questions are being addressed using a wide variety of novel techniques and datasets. In many cases, these approaches are complementary and it is likely that the most accurate picture will be generated by consolidating information relating to transcription, regulatory activity, chromatin accessibility, chromatin conformation and readouts from functional experiments, such as genome editing and reporter assays. It is clear that it will be necessary to gather this information from disease relevant cell types and conditions and that by doing so our understanding of disease etiology will be improved. This review is focused on the field of autoimmune disease functional genomics with a particular focus on the most exciting and significant research to be published within the last couple of years.
Collapse
Affiliation(s)
- James Ding
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
| | - Antonios Frantzeskos
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| |
Collapse
|
40
|
Rondanelli M, Perdoni F, Peroni G, Caporali R, Gasparri C, Riva A, Petrangolini G, Faliva MA, Infantino V, Naso M, Perna S, Rigon C. Ideal food pyramid for patients with rheumatoid arthritis: A narrative review. Clin Nutr 2020; 40:661-689. [PMID: 32928578 DOI: 10.1016/j.clnu.2020.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022]
Abstract
Emerging literature suggests that diet plays an important modulatory role in rheumatoid arthritis (RA) because diet is an environmental factor that affects inflammation, antigen presentation, antioxidant defense mechanisms and gut microbiota. Patients with RA frequently ask their doctors about which diets to follow, and even in the absence of advice from their physicians, many patients are undertaking various dietary interventions. Given this background, the aim of this review is to evaluate the evidence to date regarding the ideal dietary approach for management of RA in order to reduce the counteracting inflammation, and to construct a food pyramid for patients with RA. The pyramid shows that carbohydrates should be consumed every day (3 portions of whole grains, preferably gluten free), together with fruits and vegetables (5 portions; among which fruit, berries and citrus fruit are to be preferred, and among the vegetables, green leafy ones.), light yogurt (125 ml), skim milk (200 ml), 1 glass (125 ml) of wine and extra virgin olive oil; weekly, fish (3 portions), white meat (3 portions), legumes (2 portions) eggs (2 portions), seasoned cheeses (2 portions), and red or processed meats (once a week). At the top of the pyramid, there are two pennants: one green means that subjects with RA need some personalized supplementation (vitamin D and omega 3) and one red means that there are some foods that are banned (salt and sugar). The food pyramid allows patients to easily figure out what to eat.
Collapse
Affiliation(s)
- Mariangela Rondanelli
- IRCCS Mondino Foundation, Pavia, 27100 Italy; Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, 27100 Italy.
| | - Federica Perdoni
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona ''Istituto Santa Margherita'', University of Pavia, Pavia, 27100 Italy.
| | - Gabriella Peroni
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona ''Istituto Santa Margherita'', University of Pavia, Pavia, 27100 Italy.
| | - Roberto Caporali
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy; Clinical Rheumatology Unit Gaetano Pini Hospital, Milan 20122, Italy.
| | - Clara Gasparri
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona ''Istituto Santa Margherita'', University of Pavia, Pavia, 27100 Italy.
| | - Antonella Riva
- Research and Development Department, Indena SpA, Milan, Italy.
| | | | - Milena Anna Faliva
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona ''Istituto Santa Margherita'', University of Pavia, Pavia, 27100 Italy.
| | - Vittoria Infantino
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, 27100 Italy.
| | - Maurizio Naso
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona ''Istituto Santa Margherita'', University of Pavia, Pavia, 27100 Italy.
| | - Simone Perna
- Department of Biology, University of Bahrain, College of Science, Sakhir Campus P. O. Box 32038 Bahrain.
| | - Chiara Rigon
- Endocrinology and Nutrition Unit, Azienda di Servizi alla Persona ''Istituto Santa Margherita'', University of Pavia, Pavia, 27100 Italy.
| |
Collapse
|
41
|
Mortimer GL, Gillespie KM. Early Onset of Autoimmune Diabetes in Children with Down Syndrome-Two Separate Aetiologies or an Immune System Pre-Programmed for Autoimmunity? Curr Diab Rep 2020; 20:47. [PMID: 32839884 PMCID: PMC7445156 DOI: 10.1007/s11892-020-01318-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW An increased frequency of autoimmunity in children with Down syndrome (DS) is well described but few studies have investigated the underlying mechanisms. Recent immune system investigation of individuals with DS may shed light on the increased risk of autoimmune conditions including type 1 diabetes. RECENT FINDINGS Diagnosis of type 1 diabetes is accelerated in children with DS with 17% diagnosed at, or under, the age of 2 years compared with only 4% in the same age group in the general population. Counterintuitively, children with DS and diabetes have less human leukocyte antigen (HLA)-mediated susceptibility than age-matched children with autoimmune diabetes from the general population. Early onset of diabetes in DS is further highlighted by the recent description of neonatal cases of diabetes which is autoimmune but not HLA associated. There are two potential explanations for this accelerated onset: (1) an additional chromosome 21 increases the genetic and immunological risk of autoimmune diabetes or (2) there are two separate aetiologies in children with DS and diabetes. Autoimmunity in DS is an under-investigated area. In this review, we will draw on recent mechanistic studies in individuals with DS which shed some light on the increased risk of autoimmunity in children with DS and consider the current support for and against two aetiologies underlying diabetes in children with DS.
Collapse
Affiliation(s)
- Georgina L Mortimer
- Diabetes and Metabolism, Bristol Medical School, Level 2, Learning and Research, Southmead Hospital, University of Bristol, Bristol, BS10 5NB, UK
| | - Kathleen M Gillespie
- Diabetes and Metabolism, Bristol Medical School, Level 2, Learning and Research, Southmead Hospital, University of Bristol, Bristol, BS10 5NB, UK.
| |
Collapse
|
42
|
Zhang Y, Yang HT, Kadash-Edmondson K, Pan Y, Pan Z, Davidson BL, Xing Y. Regional Variation of Splicing QTLs in Human Brain. Am J Hum Genet 2020; 107:196-210. [PMID: 32589925 PMCID: PMC7413857 DOI: 10.1016/j.ajhg.2020.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
A major question in human genetics is how sequence variants of broadly expressed genes produce tissue- and cell type-specific molecular phenotypes. Genetic variation of alternative splicing is a prevalent source of transcriptomic and proteomic diversity in human populations. We investigated splicing quantitative trait loci (sQTLs) in 1,209 samples from 13 human brain regions, using RNA sequencing (RNA-seq) and genotype data from the Genotype-Tissue Expression (GTEx) project. Hundreds of sQTLs were identified in each brain region. Some sQTLs were shared across brain regions, whereas others displayed regional specificity. These “regionally ubiquitous” and “regionally specific” sQTLs showed distinct positional distributions of single-nucleotide polymorphisms (SNPs) within and outside essential splice sites, respectively, suggesting their regulation by distinct molecular mechanisms. Integrating the binding motifs and expression patterns of RNA binding proteins with exon splicing profiles, we uncovered likely causal variants underlying brain region-specific sQTLs. Notably, SNP rs17651213 created a putative binding site for the splicing factor RBFOX2 and was associated with increased splicing of MAPT exon 3 in cerebellar tissues, where RBFOX2 was highly expressed. Overall, our study reveals a more comprehensive spectrum and regional variation of sQTLs in human brain and demonstrates that such regional variation can be used to fine map potential causal variants of sQTLs and their associated neurological diseases.
Collapse
Affiliation(s)
- Yida Zhang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Harry Taegyun Yang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kathryn Kadash-Edmondson
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yang Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhicheng Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
43
|
Hemminki K, Huang W, Sundquist J, Sundquist K, Ji J. Autoimmune diseases and hematological malignancies: Exploring the underlying mechanisms from epidemiological evidence. Semin Cancer Biol 2020; 64:114-121. [DOI: 10.1016/j.semcancer.2019.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 02/08/2023]
|
44
|
UBASH3A deficiency accelerates type 1 diabetes development and enhances salivary gland inflammation in NOD mice. Sci Rep 2020; 10:12019. [PMID: 32694640 PMCID: PMC7374577 DOI: 10.1038/s41598-020-68956-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Recent advances in genetic analyses have significantly refined human type 1 diabetes (T1D) associated loci. The goal of such effort is to identify the causal genes and have a complete understanding of the molecular pathways that independently or interactively influence cellular processes leading to the destruction of insulin producing pancreatic β cells. UBASH3A has been suggested as the underlying gene for a human T1D associated region on chromosome 21. To further evaluate the role of UBASH3A in T1D, we targeted Ubash3a in NOD mice using zinc-finger nuclease mediated mutagenesis. In both 10-week-old females and males, significantly more advanced insulitis was observed in UBASH3A-deficient than in wild-type NOD mice. Consistently, UBASH3A-deficient NOD mice developed accelerated T1D in both sexes, which was associated with increased accumulation of β-cell autoreactive T cells in the spleen and pancreatic lymph node. Adoptive transfer of splenic T cells into NOD.Rag1-/- mice demonstrated that UBASH3A deficiency in T cells was sufficient to promote T1D development. Our results provide strong evidence to further support a role of UBASH3A in T1D. In addition to T1D, UBASH3A deficiency also promoted salivary gland inflammation in females, demonstrating its broad impact on autoimmunity.
Collapse
|
45
|
Tian Z, Song Y, Yao Y, Guo J, Gong Z, Wang Z. Genetic Etiology Shared by Multiple Sclerosis and Ischemic Stroke. Front Genet 2020; 11:646. [PMID: 32719717 PMCID: PMC7348066 DOI: 10.3389/fgene.2020.00646] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/27/2020] [Indexed: 12/23/2022] Open
Abstract
Although dramatic progress has been achieved in the understanding and treatment of multiple sclerosis (MS) and ischemic stroke (IS), more precise and instructive support is required for further research. Recent large-scale genome-wide association studies (GWASs) have already revealed risk variants for IS and MS, but the common genetic etiology between MS and IS remains an unresolved issue. This research was designed to overlapping genes between MS and IS and unmask their transcriptional features. We designed a three-section analysis process. Firstly, we computed gene-based analyses of MS GWAS and IS GWAS data sets by VGEAS2. Secondly, overlapping genes of significance were identified in a meta-analysis using the Fisher’s procedure. Finally, we performed gene expression analyses to confirm transcriptional changes. We identified 24 shared genes with Bonferroni correction (Pcombined < 2.31E-04), and five (FOXP1, CAMK2G, CLEC2D, LBH, and SLC2A4RG) had significant expression differences in MS and IS gene expression omnibus data sets. These meaningful shared genes between IS and MS shed light on the underlying genetic etiologies shared by the diseases. Our results provide a basis for in-depth genomic studies of associations between MS and IS.
Collapse
Affiliation(s)
- Zhu Tian
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Yang Song
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Yang Yao
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Jie Guo
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Zhongying Gong
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Zhiyun Wang
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| |
Collapse
|
46
|
Nguyen TH, Dobbyn A, Brown RC, Riley BP, Buxbaum JD, Pinto D, Purcell SM, Sullivan PF, He X, Stahl EA. mTADA is a framework for identifying risk genes from de novo mutations in multiple traits. Nat Commun 2020; 11:2929. [PMID: 32522981 PMCID: PMC7287090 DOI: 10.1038/s41467-020-16487-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 05/06/2020] [Indexed: 11/12/2022] Open
Abstract
Joint analysis of multiple traits can result in the identification of associations not found through the analysis of each trait in isolation. Studies of neuropsychiatric disorders and congenital heart disease (CHD) which use de novo mutations (DNMs) from parent-offspring trios have reported multiple putatively causal genes. However, a joint analysis method designed to integrate DNMs from multiple studies has yet to be implemented. We here introduce multiple-trait TADA (mTADA) which jointly analyzes two traits using DNMs from non-overlapping family samples. We first demonstrate that mTADA is able to leverage genetic overlaps to increase the statistical power of risk-gene identification. We then apply mTADA to large datasets of >13,000 trios for five neuropsychiatric disorders and CHD. We report additional risk genes for schizophrenia, epileptic encephalopathies and CHD. We outline some shared and specific biological information of intellectual disability and CHD by conducting systems biology analyses of genes prioritized by mTADA.
Collapse
Affiliation(s)
- Tan-Hoang Nguyen
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA.
| | - Amanda Dobbyn
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth C Brown
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Brien P Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Joseph D Buxbaum
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalila Pinto
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shaun M Purcell
- Sleep Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, USA.
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
47
|
Bokhari HA, Shaik NA, Banaganapalli B, Nasser KK, Ageel HI, Al Shamrani AS, Rashidi OM, Al Ghubayshi OY, Shaik J, Ahmad A, Alrayes NM, Al-Aama JY, Elango R, Saadah OI. Whole exome sequencing of a Saudi family and systems biology analysis identifies CPED1 as a putative causative gene to Celiac Disease. Saudi J Biol Sci 2020; 27:1494-1502. [PMID: 32489286 PMCID: PMC7254030 DOI: 10.1016/j.sjbs.2020.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 12/15/2022] Open
Abstract
Celiac disease (CD) is a gastrointestinal disorder whose genetic basis is not fully understood. Therefore, we studied a Saudi family with two CD affected siblings to discover the causal genetic defect. Through whole exome sequencing (WES), we identified that both siblings have inherited an extremely rare and deleterious CPED1 genetic variant (c.241 A > G; p.Thr81Ala) segregating as autosomal recessive mutation, suggesting its putative causal role in the CD. Saudi population specific minor allele frequency (MAF) analysis has confirmed its extremely rare prevalence in homozygous condition (MAF is 0.0004). The Sanger sequencing analysis confirmed the absence of this homozygous variant in 100 sporadic Saudi CD cases. Genotype-Tissue Expression (GTEx) data has revealed that CPED1 is abundantly expressed in gastrointestinal mucosa. By using a combination of systems biology approaches like protein 3D modeling, stability analysis and nucleotide sequence conservation analysis, we have further established that this variant is deleterious to the structural and functional aspects of CPED1 protein. To the best of our knowledge, this variant has not been previously reported in CD or any other gastrointestinal disease. The cell culture and animal model studies could provide further insight into the exact role of CPED1 p.Thr81Ala variant in the pathophysiology of CD. In conclusion, by using WES and systems biology analysis, present study for the first-time reports CPED1 as a potential causative gene for CD in a Saudi family with potential implications to both disease diagnosis and genetic counseling.
Collapse
Affiliation(s)
- Hifaa A Bokhari
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalidah Khalid Nasser
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ali Saad Al Shamrani
- Department of Pedidatrics, Maternity and Children Hospital, Makkah, Saudi Arabia
| | - Omran M Rashidi
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | | | - Jilani Shaik
- Dept of Biochemistry, Genome Research Chair, Faculty of Science, King Saud University, Saudi Arabia
| | - Aftab Ahmad
- Department of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Mohammad Alrayes
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jumana Yousuf Al-Aama
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Omar Ibrahim Saadah
- Pediatric Gastroenterology Unit, Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
48
|
A cross-disease meta-GWAS identifies four new susceptibility loci shared between systemic sclerosis and Crohn's disease. Sci Rep 2020; 10:1862. [PMID: 32024964 PMCID: PMC7002703 DOI: 10.1038/s41598-020-58741-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified a number of genetic risk loci associated with systemic sclerosis (SSc) and Crohn’s disease (CD), some of which confer susceptibility to both diseases. In order to identify new risk loci shared between these two immune-mediated disorders, we performed a cross-disease meta-analysis including GWAS data from 5,734 SSc patients, 4,588 CD patients and 14,568 controls of European origin. We identified 4 new loci shared between SSc and CD, IL12RB2, IRF1/SLC22A5, STAT3 and an intergenic locus at 6p21.31. Pleiotropic variants within these loci showed opposite allelic effects in the two analysed diseases and all of them showed a significant effect on gene expression. In addition, an enrichment in the IL-12 family and type I interferon signaling pathways was observed among the set of SSc-CD common genetic risk loci. In conclusion, through the first cross-disease meta-analysis of SSc and CD, we identified genetic variants with pleiotropic effects on two clinically distinct immune-mediated disorders. The fact that all these pleiotropic SNPs have opposite allelic effects in SSc and CD reveals the complexity of the molecular mechanisms by which polymorphisms affect diseases.
Collapse
|
49
|
STAT4 sequence variant and elevated gene expression are associated with type 1 diabetes in Polish children. Cent Eur J Immunol 2020; 45:22-28. [PMID: 32425676 PMCID: PMC7226553 DOI: 10.5114/ceji.2019.92492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/23/2019] [Indexed: 12/23/2022] Open
Abstract
Introduction Type 1 diabetes (T1D) is caused by the autoimmune destruction of pancreatic β cells, resulting from coincident genetic predisposition and some environmental triggers. Signal transducer and activator of transcription 4 (STAT4) gene encodes a transcription factor, which promotes Th1 cell differentiation, interferon γ production, and development of Th17 cells. Polymorphisms of STAT4 are associated with several autoimmune conditions, while studies in T1D provided inconsistent results. This analysis was designed to investigate the association of STAT4 rs7574865 with T1D in Polish children and to assess STAT4 expression in newly diagnosed subjects. Material and methods Rs7574865 was genotyped in 656 T1D children and 782 healthy individuals. STAT4 mRNA expression was analyzed in peripheral blood mononuclear cells (PBMCs) from 29 children with T1D and 27 age-matched controls. β-cell and thyroid-specific serum autoantibodies were assessed with radioimmunoassays. Results The distribution of rs7574865 genotypes and alleles demonstrated significant difference (p = 0.002, p < 0.001, respectively) between patients vs. controls. Carriers of the minor T allele presented earlier T1D onset (p = 0.017). No differences were found in γ-cell autoantibody in genotype-stratified patients (p > 0.050), while anti-thyroid antibodies were more frequent in carriers of the minor allele(p = 0.039 for anti-thyroperoxidase, p = 0.007 for anti-thyroglobulin antibodies, respectively). STAT4 was overexpressed in PBMCs from T1D patients (p = 0.008), especially subjects with two/three circulating β-cell antibodies (p < 0.001). Conclusions The study confirms an association of STAT4 rs7574865 with T1D in Polish patients, and provides an evidence for its relationship with an earlier disease onset and concomitant thyroid autoimmunity. STAT4 expression appears elevated in T1D, especially with more severe reaction against β-cell antigens.
Collapse
|
50
|
Ge Y, Paisie TK, Chen S, Concannon P. UBASH3A Regulates the Synthesis and Dynamics of TCR-CD3 Complexes. THE JOURNAL OF IMMUNOLOGY 2019; 203:2827-2836. [PMID: 31659016 DOI: 10.4049/jimmunol.1801338] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 09/27/2019] [Indexed: 01/14/2023]
Abstract
The TCR-CD3 complex is a multicomponent membrane receptor, the expression of which is tightly regulated in thymocytes, as well as in mature T cells both at steady state and upon stimulation. In this study, we report novel roles for UBASH3A in TCR-CD3 synthesis and turnover. UBASH3A is a negative regulator of T cell function and plays a broad role in autoimmunity. We show that modulation of UBASH3A levels in unstimulated Jurkat cells leads to altered amounts of total cellular CD3 chains and of cell-surface TCR-CD3 complexes; in contrast, UBASH3A does not affect the level of cell-surface CD28, an important T cell costimulatory receptor. Upon TCR engagement, UBASH3A enhances the downmodulation of cell-surface TCR-CD3. Mass spectrometry and protein-protein interaction studies uncover novel associations between UBASH3A and components of several cellular pathways involved in the regulation of TCR-CD3 turnover and dynamics, including endoplasmic reticulum-associated protein degradation, cell motility, endocytosis, and endocytic recycling of membrane receptors. Finally, we demonstrate that the SH3 domain of UBASH3A mediates its binding to CBL-B, an E3 ubiquitin ligase that negatively regulates CD28-mediated signaling and, hence, T cell activation. In summary, this study provides new mechanistic insights into how UBASH3A regulates T cell activation and contributes to autoimmunity. The interaction between UBASH3A and CBL-B may synergistically inhibit T cell function and affect risk for type 1 diabetes, as both genes have been shown to be associated with this autoimmune disease.
Collapse
Affiliation(s)
- Yan Ge
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610; .,Genetics Institute, University of Florida, Gainesville, FL 32610
| | - Taylor K Paisie
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.,Genetics Institute, University of Florida, Gainesville, FL 32610.,Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32610
| | - Sixue Chen
- Genetics Institute, University of Florida, Gainesville, FL 32610.,Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32610.,Department of Biology, University of Florida, Gainesville, FL 32611.,Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611; and.,Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610
| | - Patrick Concannon
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610; .,Genetics Institute, University of Florida, Gainesville, FL 32610
| |
Collapse
|