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Olayinka-Adefemi F, Hou S, Marshall AJ. Dual inhibition of phosphoinositide 3-kinases delta and gamma reduces chronic B cell activation and autoantibody production in a mouse model of lupus. Front Immunol 2023; 14:1115244. [PMID: 37234154 PMCID: PMC10206234 DOI: 10.3389/fimmu.2023.1115244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Phosphoinositide 3-kinase delta (PI3Kδ) plays key roles in normal B cell activation and is chronically activated in malignant B cells. Targeting of PI3Kδ using FDA-approved drugs Idelalisib or Umbralisib has shown efficacy in treatment of multiple B cell malignancies. Duvelisib, an inhibitor targeting both PI3Kδ and PI3Kγ (PI3Kδγi) has also been used for treatment of several leukemias and lymphomas and was suggested to offer potential additional benefits in supressing T cell and inflammatory responses. Transcriptomics analyses indicated that while most B cell subsets predominantly express PI3Kδ, plasma cells upregulate PI3Kγ. We thus assessed whether PI3Kδγi treatment can impact chronic B cell activation in the context of an autoantibody-mediated disease. Using the TAPP1R218LxTAPP2R211L (TAPP KI) mouse model of lupus-like disease driven by dysregulated PI3K pathway activity, we performed 4 week PI3Kδγi treatments and found significant reduction in CD86+ B cells, germinal center B cells, follicular helper T cells and plasma cells in multiple tissues. This treatment also significantly attenuated the abnormally elevated serum levels of IgG isotypes observed in this model. The profile of autoantibodies generated was markedly altered by PI3Kδγi treatment, with significant reductions in IgM and IgG targeting nuclear antigens, matrix proteins and other autoantigens. Kidney pathology was also impacted, with reduced IgG deposition and glomerulonephritis. These results indicate that dual inhibition of PI3Kδ and PI3Kγ can target autoreactive B cells and may have therapeutic benefits in autoantibody-mediated disease.
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Kortam MA, Elfar N, Shaker OG, El-Boghdady NA, Abd-Elmawla MA. MAGI2-AS3 and miR-374b-5p as Putative Regulators of Multiple Sclerosis via Modulating the PTEN/AKT/IRF-3/IFN-β Axis: New Clinical Insights. ACS Chem Neurosci 2023; 14:1107-1118. [PMID: 36878000 DOI: 10.1021/acschemneuro.2c00653] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic disease and one of the leading causes of disability in young adults. The current study aims to investigate the pathogenesis of MS via studying the regulatory role of novel lncRNA MAGI2-AS3 in miR-374b-5p and their downstream targets PTEN/AKT/IRF-3/IFN-β and the relationship of this pathway with disease severity. Moreover, it aims to assess the role of MAGI2-AS3/miR-374b-5p as diagnostic and/or prognostic biomarkers for MS. Overall, 150 contributors were recruited: 100 patients with MS and 50 healthy volunteers. Gene expression of MAGI2-AS3, miR-374b-5p, PTEN, AKT, and IRF-3 were assessed using RT-qPCR, and IFN-β was measured by ELISA. Compared with the healthy control group, serum MAGI2-AS3 and PTEN were downregulated in MS patients, whereas miR-374b-5p, PI3K, AKT, IRF-3, and IFN-β were upregulated in MS patients. Furthermore, MAGI2-AS3 was downregulated, while miR-374b-5p was upregulated in MS patients with an expanded disability status scale (EDSS) ≥3.5, compared to patients with an EDSS <3.5. Receiver-operating-characteristic curve analysis revealed that MAGI2-AS3 and miR-374b-5p can be used in the diagnosis of MS. Remarkably, multivariate logistic analysis revealed that MAGI2-AS3, miR-374b-5p, PTEN, and AKT act as independent variables in MS. Moreover, MAGI2-AS3 was directly correlated with PTEN and inversely correlated with miR-374b-5p, AKT, and EDSS. Regarding miR-374b-5p, it was positively correlated with AKT and EDSS. In conclusion, the study showed for the first time that the crosstalk between MAGI2-AS3 and miR-374b-5p could affect the AKT/IRF3/IFN-β axis in MS. Interestingly, MAGI2-AS3 and miR-374b-5p could be genetic noninvasive biomarkers for MS.
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Affiliation(s)
- Mona A Kortam
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Nourhan Elfar
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo 11578, Egypt
- Egyptian Drug Authority (EDA), Ministry of Health and Population, Cairo 11567, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo 11562, Egypt
| | - Noha A El-Boghdady
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Mai A Abd-Elmawla
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
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Tabouni M, Ali A, Aljaberi N, Alblooshi H. Lupus nephritis: A focus on the United Arab Emirates and the potential role of genetics. Lupus 2022; 31:1415-1422. [PMID: 36017600 DOI: 10.1177/09612033221122982] [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: 11/16/2022]
Abstract
Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus (SLE), characterized by chronic and progressive inflammation of the kidneys. As with many other autoimmune diseases, LN is a multifactorial disease caused by genetic and environmental factors. Globally, LN can affect around 60% of SLE patients, and it was observed to be less frequent and severe in Caucasian patients compared to other ethnic groups, including Arabs. Data on LN in the United Arab Emirates (UAE) are scattered and scarce in literature. Nevertheless, LN is common, occurring in around 43%-55% of SLE patients in the UAE. Anecdotally, the demographics and clinical features of SLE in the UAE have been distinct. However, the paucity of supporting literature makes it difficult to draw meaningful conclusions. Over the past two decades, there have been improvements in understanding the pathogenesis of LN; however, many cellular and molecular mechanisms which are implicated in the disease development and progression remain ambiguous. Investigating the clinical, pathological, and genetic characteristics of LN in different cohorts of patients is of importance for a better understanding of its pathogenesis, and thus improving its outcome. As a result, we acknowledge the need for large-scale epidemiological, clinical, and genetic investigation of LN cohorts in the UAE and surrounding regions.
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Affiliation(s)
- Mohammed Tabouni
- Department of Genetics and Genomics, College of Medicine and Health Sciences, 62776United Arab Emirates University, Al Ain, United Arab Emirates
| | - Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, 62776United Arab Emirates University, Al Ain, United Arab Emirates
| | - Najla Aljaberi
- Department of Pediatrics, College of Medicine and Health Sciences, 62776United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hiba Alblooshi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, 62776United Arab Emirates University, Al Ain, United Arab Emirates
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Harley ITW, Allison K, Scofield RH. Polygenic autoimmune disease risk alleles impacting B cell tolerance act in concert across shared molecular networks in mouse and in humans. Front Immunol 2022; 13:953439. [PMID: 36090990 PMCID: PMC9450536 DOI: 10.3389/fimmu.2022.953439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
Most B cells produced in the bone marrow have some level of autoreactivity. Despite efforts of central tolerance to eliminate these cells, many escape to periphery, where in healthy individuals, they are rendered functionally non-responsive to restimulation through their antigen receptor via a process termed anergy. Broad repertoire autoreactivity may reflect the chances of generating autoreactivity by stochastic use of germline immunoglobulin gene segments or active mechanisms may select autoreactive cells during egress to the naïve peripheral B cell pool. Likewise, it is unclear why in some individuals autoreactive B cell clones become activated and drive pathophysiologic changes in autoimmune diseases. Both of these remain central questions in the study of the immune system(s). In most individuals, autoimmune diseases arise from complex interplay of genetic risk factors and environmental influences. Advances in genome sequencing and increased statistical power from large autoimmune disease cohorts has led to identification of more than 200 autoimmune disease risk loci. It has been observed that autoantibodies are detectable in the serum years to decades prior to the diagnosis of autoimmune disease. Thus, current models hold that genetic defects in the pathways that control autoreactive B cell tolerance set genetic liability thresholds across multiple autoimmune diseases. Despite the fact these seminal concepts were developed in animal (especially murine) models of autoimmune disease, some perceive a disconnect between human risk alleles and those identified in murine models of autoimmune disease. Here, we synthesize the current state of the art in our understanding of human risk alleles in two prototypical autoimmune diseases - systemic lupus erythematosus (SLE) and type 1 diabetes (T1D) along with spontaneous murine disease models. We compare these risk networks to those reported in murine models of these diseases, focusing on pathways relevant to anergy and central tolerance. We highlight some differences between murine and human environmental and genetic factors that may impact autoimmune disease development and expression and may, in turn, explain some of this discrepancy. Finally, we show that there is substantial overlap between the molecular networks that define these disease states across species. Our synthesis and analysis of the current state of the field are consistent with the idea that the same molecular networks are perturbed in murine and human autoimmune disease. Based on these analyses, we anticipate that murine autoimmune disease models will continue to yield novel insights into how best to diagnose, prognose, prevent and treat human autoimmune diseases.
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Affiliation(s)
- Isaac T. W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
- Rheumatology Section, Medicine Service, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
| | - Kristen Allison
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
| | - R. Hal Scofield
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Medical/Research Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK, United States
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Chen X, Xu Y, Chen Q, Zhang H, Zeng Y, Geng Y, Shen L, Li F, Chen L, Chen GQ, Huang C, Liu J. The phosphatase PTEN links platelets with immune regulatory functions of mouse T follicular helper cells. Nat Commun 2022; 13:2762. [PMID: 35589797 PMCID: PMC9120038 DOI: 10.1038/s41467-022-30444-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/30/2022] [Indexed: 01/10/2023] Open
Abstract
Beyond a function in hemostasis and thrombosis, platelets can regulate innate and adaptive immune responses. Hyperactive platelets are frequently associated with multiple human autoimmune diseases, yet their pathogenic functions in these diseases have not been fully established. Emerging studies show an essential function of the phosphatase and tensin homolog (PTEN) in maintenance of immune homeostasis. Here, we show that mice with platelet-specific deletion of Pten, develop age-related lymphoproliferative diseases and humoral autoimmunity not seen in wildtype animals. Platelet-specific Pten-deficient mice have aberrant T cell activation, excessive T follicular helper (Tfh) cell responses and accumulation of platelet aggregates in lymph nodes. Transferred Pten-deficient platelets are able to infiltrate into the peripheral lymphoid tissues and form more aggregates. Moreover, Pten-deficient platelets are hyperactive and overproduce multiple Tfh-promoting cytokines via activation of the PDK1/mTORC2-AKT-SNAP23 pathway. Pten-deficient platelets show enhanced interaction with CD4+ T cells and promote conversion of CD4+ T cells into Tfh cells. Our results implicate PTEN in platelet-mediated immune homeostasis, and provide evidence that hyperactive platelets function as an important mediator in autoimmune diseases using mouse models.
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Affiliation(s)
- Xue Chen
- School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China.
| | - Yanyan Xu
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Qidi Chen
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Heng Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Yu Zeng
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Yan Geng
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Lei Shen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Fubin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Lei Chen
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Guo-Qiang Chen
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
| | - Junling Liu
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.
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Harley ITW, Sawalha AH. Systemic lupus erythematosus as a genetic disease. Clin Immunol 2022; 236:108953. [PMID: 35149194 PMCID: PMC9167620 DOI: 10.1016/j.clim.2022.108953] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus is the prototypical systemic autoimmune disease, as it is characterized both by protean multi-organ system manifestations and by the uniform presence of pathogenic autoantibodies directed against components of the nucleus. Prior to the modern genetic era, the diverse clinical manifestations of SLE suggested to many that SLE patients were unlikely to share a common genetic risk basis. However, modern genetic studies have revealed that SLE usually arises when an environmental exposure occurs in an individual with a collection of genetic risk variants passing a liability threshold. Here, we summarize the current state of the field aimed at: (1) understanding the genetic architecture of this complex disease, (2) synthesizing how this genetic risk architecture impacts cellular and molecular disease pathophysiology, (3) providing illustrative examples that highlight the rich complexity of the pathobiology of this prototypical autoimmune disease and (4) communicating this complex etiopathogenesis to patients.
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Affiliation(s)
- Isaac T W Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; Human Immunology and Immunotherapy Initiative (HI(3)), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA; Rocky Mountain Regional Veteran's Administration Medical Center (VAMC), Medicine Service, Rheumatology Section, Aurora, CO, USA.
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA; Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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7
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Grammatikopoulos T, Hadzic N, Foskett P, Strautnieks S, Samyn M, Vara R, Dhawan A, Hertecant J, Al Jasmi F, Rahman O, Deheragoda M, Bull LN, Thompson RJ. Liver Disease and Risk of Hepatocellular Carcinoma in Children With Mutations in TALDO1. Hepatol Commun 2022; 6:473-479. [PMID: 34677006 PMCID: PMC8870026 DOI: 10.1002/hep4.1824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mutations in the transaldolase 1 (TALDO1) gene have been described in a limited number of cases. Several organs can be affected and clinical manifestations are variable, but often include liver dysfunction and/or hepatosplenomegaly. We report 4 patients presenting with liver disease: 2 with early-onset hepatocellular carcinoma (HCC). Patients with cholestasis and mutations in TALDO1 were identified by next-generation sequencing. Clinical, laboratory, and histological data were collected. Four (1 male) patients were identified with variants predicted to be damaging in TALDO1. Three patients were homozygous (two protein truncating/one missense mutations), 1 one was compound heterozygous (two missense mutations). Median age at presentation was 4 months (range, 2-210 days) with jaundice (3), hepatosplenomegaly (3), and pancytopaenia (1). The diagnosis was corroborated by detection of minimal transaldolase enzyme activity in skin fibroblasts in two cases and raised urine polyols in the third. Three patients underwent liver transplantation (LT), 2 of whom had confirmed HCC on explanted liver. One patient suddenly died shortly after LT. The nontransplanted case has a chronic liver disease with multiple dysplastic liver nodules, but normal liver biochemistry and alpha-fetoprotein. Median follow-up was 4 years (range, 1-21). Conclusion: Transaldolase deficiency can include early-onset normal gamma-glutamyltransferase liver disease with multisystem involvement and variable progression. Patients with this disease are at risk of early-onset HCC and may require early LT.
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Affiliation(s)
- Tassos Grammatikopoulos
- Pediatric Liver, GI & Nutrition Center and MowatLabsKing's College HospitalLondonUnited Kingdom.,Institute of Liver StudiesKing's College LondonLondonUnited Kingdom
| | - Nedim Hadzic
- Pediatric Liver, GI & Nutrition Center and MowatLabsKing's College HospitalLondonUnited Kingdom
| | - Pierre Foskett
- Institute of Liver StudiesKing's College HospitalLondonUnited Kingdom
| | | | - Marianne Samyn
- Pediatric Liver, GI & Nutrition Center and MowatLabsKing's College HospitalLondonUnited Kingdom
| | - Roshni Vara
- Department of Pediatric Inherited Metabolic DiseasesEvelina Children's HospitalLondonUnited Kingdom
| | - Anil Dhawan
- Pediatric Liver, GI & Nutrition Center and MowatLabsKing's College HospitalLondonUnited Kingdom
| | - Jozef Hertecant
- Division of Genetics/MetabolicsDepartment of PediatricsTawam HospitalAl AinUnited Arab Emirates
| | - Fatma Al Jasmi
- Division of Genetics/MetabolicsDepartment of PediatricsTawam HospitalAl AinUnited Arab Emirates
| | - Obydur Rahman
- Institute of Liver StudiesKing's College HospitalLondonUnited Kingdom
| | - Maesha Deheragoda
- Institute of Liver StudiesKing's College HospitalLondonUnited Kingdom
| | - Laura N Bull
- Institute for Human Genetics and Liver Center LaboratoryDepartment of MedicineUniversity of California San FranciscoSan FranciscoCAUSA
| | - Richard J Thompson
- Pediatric Liver, GI & Nutrition Center and MowatLabsKing's College HospitalLondonUnited Kingdom.,Institute of Liver StudiesKing's College LondonLondonUnited Kingdom
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8
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Wu Q, Qin Y, Shi M, Yan L. Diagnostic significance of circulating miR-485-5p in patients with lupus nephritis and its predictive value evaluation for the clinical outcomes. J Chin Med Assoc 2021; 84:491-497. [PMID: 33742995 DOI: 10.1097/jcma.0000000000000522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Lupus nephritis (LN) is one of the main risk factors contributing to morbidity and mortality of systemic lupus erythematosus (SLE). This study aimed to investigate the potential role of miR-485-5p in human LN. METHODS Quantitative real-time polymerase chain reaction was used for the measurement of miR-485-5p levels. The levels of interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) in serum were determined by enzyme-linked immunosorbent assay. The diagnostic role of miR-485-5p in LN was evaluated by the receiver operating characteristic (ROC) curve. The impact of miR-485-5p on end-stage renal disease (ESRD) was compared by Kaplan-Meier analysis and Cox regression analysis. The target gene was determined by a dual-luciferase reporter assay system. RESULTS MiR-485-5p was highly expressed in SLE and LN patients compared with the healthy controls, and LN patients had the highest level of miR-485-5p. The expression level of miR-485-5p in active LN patients was significantly increased compared with that in nonactive cases. MiR-485-5p expression showed a positive correlation with the levels of estimated glomerular filtration rate, serum creatinine, proteinuria, SLE disease activity index score, and inflammatory cytokines. The ROC analysis results indicated that serum miR-485-5p was a promising biomarker for the early diagnosis of LN, and it can distinguish active LN patients from nonactive ones. Phosphatase and tensin homolog was a direct target of miR-485-5p, and negatively associated with serum miR-485-5p levels. More ESRD events were observed in cases with high miR-485-5p expression, miR-485-5p was an independent factor for the risk of ESRD in LN patients. CONCLUSION Serum miR-485-5p might be a novel promising diagnostic marker for LN and has potential predictive value for ESRD risk in LN patients.
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Affiliation(s)
- Qinghua Wu
- Department of Nephrology, Dongying People's Hospital, Dongying, Shandong, China
| | - Yanan Qin
- Department of Obstetrics, Dongying People's Hospital, Dongying, Shandong, China
| | - Mei Shi
- Department of Nephrology, Dongying People's Hospital, Dongying, Shandong, China
| | - Liping Yan
- Department of Outpatient, Dongying People's Hospital, Dongying, Shandong, China
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Li B, Dong J, Yu J, Fan Y, Shang L, Zhou X, Bai Y. Pinpointing miRNA and genes enrichment over trait-relevant tissue network in Genome-Wide Association Studies. BMC Med Genomics 2020; 13:191. [PMID: 33371893 PMCID: PMC7771066 DOI: 10.1186/s12920-020-00830-w] [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: 10/25/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Understanding gene regulation is important but difficult. Elucidating tissue-specific gene regulation mechanism is even more challenging and requires gene co-expression network assembled from protein-protein interaction, transcription factor and gene binding, and post-transcriptional regulation (e.g., miRNA targeting) information. The miRNA binding affinity could therefore be changed by SNP(s) located at the 3' untranslated regions (3'UTR) of the target messenger RNA (mRNA) which miRNA(s) interacts with. Genome-wide association study (GWAS) has reported significant numbers of loci hosting SNPs associated with many traits. The goal of this study is to pinpoint GWAS functional variants located in 3'UTRs and elucidate if the genes harboring these variants along with their targeting miRNAs are associated with genetic traits relevant to certain tissues. METHODS By applying MIGWAS, CoCoNet, ANNOVAR, and DAVID bioinformatics software and utilizing the gene expression database (e.g. GTEx data) to study GWAS summary statistics for 43 traits from 28 GWAS studies, we have identified a list of miRNAs and targeted genes harboring 3'UTR variants, which could contribute to trait-relevant tissue over miRNA-target gene network. RESULTS Our result demonstrated that strong association between traits and tissues exists, and in particular, the Primary Biliary Cirrhosis (PBC) trait has the most significant p-value for all 180 tissues among all 43 traits used for this study. We reported SNPs located in 3'UTR regions of genes (SFMBT2, ZC3HAV1, and UGT3A1) targeted by miRNAs for PBC trait and its tissue association network. After employing Gene Ontology (GO) analysis for PBC trait, we have also identified a very important miRNA targeted gene over miRNA-target gene network, PFKL, which encodes the liver subunit of an enzyme. CONCLUSIONS The non-coding variants identified from GWAS studies are casually assumed to be not critical to translated protein product. However, 3' untranslated regions (3'UTRs) of genes harbor variants can often change the binding affinity of targeting miRNAs playing important roles in protein translation degree. Our study has shown that GWAS variants could play important roles on miRNA-target gene networks by contributing the association between traits and tissues. Our analysis expands our knowledge on trait-relevant tissue network and paves way for future human disease studies.
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Affiliation(s)
- Binze Li
- Bellaire High School, 5100 Maple St, Bellaire, TX, 77401, USA
| | - Julian Dong
- Northville High School, 45700 Six Mile Road, Northville, MI, 48168, USA
| | - Jiaqi Yu
- College Preparatory School, 6100 Broadway, Oakland, CA, 94618, USA
| | - Yuqi Fan
- The Master's Academy, 1500 Lukas Ln, Oviedo, FL, 32765, USA
| | - Lulu Shang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.,Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, 48197, USA. .,Next-Gen Intelligent Science Training, Ann Arbor, MI, 48105, USA.
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