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Feng Q, Xu K, Shah M, Li S, Leavitt AD, Godley LA, De Smith AJ, Wiemels JL. Evaluation of the genetic basis of familial-associated early-onset hematologic cancers in an ancestral/ethnically diverse population. Haematologica 2024; 109:2085-2091. [PMID: 38205536 PMCID: PMC11215364 DOI: 10.3324/haematol.2023.284224] [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: 09/20/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Genetic predisposition to hematologic malignancies has historically been addressed utilizing patients recruited from clinical trials and pedigrees constructed at major treatment centers. Such efforts leave unexplored the genetic basis of variations in risk by race/ethnic group shown in population-based surveillance data where cancer registration, compulsory by law, delivers universal enrollment. To address this, we performed exome sequencing on DNA isolated from newborn bloodspots derived from sibling pairs with early-onset cancers across California in which at least one of the siblings developed a hematologic cancer, using unbiased recruitment from the full state population. We identified pathogenic/likely pathogenic (P/ LP) variants among 1,172 selected cancer genes that were private or present at low allele frequencies in reference populations. Within 64 subjects from 32 families, we found 9 LP variants shared between siblings, and an additional 7 such variants in singleton children (not shared with their sibling). In 8 of the shared cases, the ancestral origin of the local haplotype that carries P/LP variants matched the dominant global ancestry of study participant families. This was the case for Latino sibling pairs on FLG and CBLB, non-Latino White sibling pairs in TP53 and NOD2, and a shared GATA2 variant for a non-Latino Black sibling pair. A new inherited mutation in HABP2 was identified in a sibling pair, one with diffuse large B-cell lymphoma and the other with neuroblastoma. Overall, the profile of P/LP germline variants across ancestral/ethnic groups suggests that rare alleles contributing to hematologic diseases originate within their race/ethnic origin parental populations, demonstrating the value of this discovery process in diverse, population-based registries.
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Affiliation(s)
- Qianxi Feng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Keren Xu
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Mancy Shah
- Division of Hematology/Oncology, Department of Medicine, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Andrew D Leavitt
- Departments of Medicine and Laboratory Medicine, University of California, San Francisco, San Francisco, CA
| | - Lucy A Godley
- Division of Hematology/Oncology, Department of Medicine, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Adam J De Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA.
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Bondar G, Mahapatra AD, Bao TM, Silacheva I, Hairapetian A, Vu T, Su S, Katappagari A, Galan L, Chandran J, Adamov R, Mancusi L, Lai I, Rahman A, Grogan T, Hsu JJ, Cappelletti M, Ping P, Elashoff D, Reed EF, Deng MC. An Exercise Immune Fitness Test to Unravel Disease Mechanisms-A Proof-of-Concept Heart Failure Study. J Clin Med 2024; 13:3200. [PMID: 38892912 PMCID: PMC11172881 DOI: 10.3390/jcm13113200] [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: 05/14/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Background: Cardiorespiratory fitness positively correlates with longevity and immune health. Regular exercise may provide health benefits by reducing systemic inflammation. In chronic disease conditions, such as chronic heart failure and chronic fatigue syndrome, mechanistic links have been postulated between inflammation, muscle weakness, frailty, catabolic/anabolic imbalance, and aberrant chronic activation of immunity with monocyte upregulation. We hypothesize that (1) temporal changes in transcriptome profiles of peripheral blood mononuclear cells during strenuous acute bouts of exercise using cardiopulmonary exercise testing are present in adult subjects, (2) these temporal dynamic changes are different between healthy persons and heart failure patients and correlate with clinical exercise-parameters and (3) they portend prognostic information. Methods: In total, 16 Heart Failure (HF) patients and 4 healthy volunteers (HV) were included in our proof-of-concept study. All participants underwent upright bicycle cardiopulmonary exercise testing. Blood samples were collected at three time points (TP) (TP1: 30 min before, TP2: peak exercise, TP3: 1 h after peak exercise). We divided 20 participants into 3 clinically relevant groups of cardiorespiratory fitness, defined by peak VO2: HV (n = 4, VO2 ≥ 22 mL/kg/min), mild HF (HF1) (n = 7, 14 < VO2 < 22 mL/kg/min), and severe HF (HF2) (n = 9, VO2 ≤ 14 mL/kg/min). Results: Based on the statistical analysis with 20-100% restriction, FDR correction (p-value 0.05) and 2.0-fold change across the three time points (TP1, TP2, TP3) criteria, we obtained 11 differentially expressed genes (DEG). Out of these 11 genes, the median Gene Expression Profile value decreased from TP1 to TP2 in 10 genes. The only gene that did not follow this pattern was CCDC181. By performing 1-way ANOVA, we identified 8/11 genes in each of the two groups (HV versus HF) while 5 of the genes (TTC34, TMEM119, C19orf33, ID1, TKTL2) overlapped between the two groups. We found 265 genes which are differentially expressed between those who survived and those who died. Conclusions: From our proof-of-concept heart failure study, we conclude that gene expression correlates with VO2 peak in both healthy individuals and HF patients, potentially by regulating various physiological processes involved in oxygen uptake and utilization during exercise. Multi-omics profiling may help identify novel biomarkers for assessing exercise capacity and prognosis in HF patients, as well as potential targets for therapeutic intervention to improve VO2 peak and quality of life. We anticipate that our results will provide a novel metric for classifying immune health.
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Affiliation(s)
- Galyna Bondar
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | | | - Tra-Mi Bao
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Irina Silacheva
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Adrian Hairapetian
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Thomas Vu
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Stephanie Su
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Ananya Katappagari
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Liana Galan
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Joshua Chandran
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Ruben Adamov
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Lorenzo Mancusi
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Isabel Lai
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Anca Rahman
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Tristan Grogan
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Jeffrey J. Hsu
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Monica Cappelletti
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Peipei Ping
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - David Elashoff
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Elaine F. Reed
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
| | - Mario C. Deng
- David Geffen School of Medicine, University of California Los Angeles Medical Center, Los Angeles, CA 90095, USA; (G.B.); (T.-M.B.); (I.S.); (A.H.); (T.V.); (S.S.); (A.K.); (L.G.); (J.C.); (R.A.); (L.M.); (I.L.); (A.R.); (T.G.); (J.J.H.); (M.C.); (P.P.); (D.E.); (E.F.R.)
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Dong X, Gong LL, Hong MZ, Pan JS. Investigating the shared genetic architecture between primary sclerosing cholangitis and inflammatory bowel diseases: a Mendelian randomization study. BMC Gastroenterol 2024; 24:77. [PMID: 38373892 PMCID: PMC10875759 DOI: 10.1186/s12876-024-03162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Several studies have found that primary sclerosing cholangitis (PSC) and inflammatory bowel disease (IBD) are closely associated. However, the direction and causality of their interactions remain unclear. Thus, this study employs Mendelian Randomization to explore whether there are causal associations of genetically predicted PSC with IBD. METHODS Genetic variants associated with the genome-wide association study (GWAS) of PSC were used as instrumental variables. The statistics for IBD, including ulcerative colitis (UC), and Crohn's disease (CD) were derived from GWAS. Then, five methods were used to estimate the effects of genetically predicted PSC on IBD, including MR Egger, Weighted median (WM), Inverse variance weighted (IVW), Simple mode, and Weighted mode. Last, we also evaluated the pleiotropic effects, heterogeneity, and a leave-one-out sensitivity analysis that drives causal associations to confirm the validity of the analysis. RESULTS Genetically predicted PSC was significantly associated with an increased risk of UC, according to the study (odds ratio [OR] IVW= 1.0014, P<0.05). However, none of the MR methods found significant causal evidence of genetically predicted PSC in CD (All P>0.05). The sensitivity analysis results showed that the causal effect estimations of genetically predicted PSC on IBD were robust, and there was no horizontal pleiotropy or statistical heterogeneity. CONCLUSIONS Our study corroborated a causal association between genetically predicted PSC and UC but did not between genetically predicted PSC and CD. Then, we identification of shared SNPs for PSC and UC, including rs3184504, rs9858213, rs725613, rs10909839, and rs4147359. More animal experiments and clinical observational studies are required to further clarify the underlying mechanisms of PSC and IBD.
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Affiliation(s)
- Xuan Dong
- Department of Hepatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Hepatology Research Institute, Fujian Medical University, Fuzhou, Fujian, China
- Department of Hepatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hosptial, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Clinical Research Center for Hepatopathy and Intestinal Diseases, Fuzhou, Fujian, China
| | - Li-Li Gong
- Department of General Practice, Zhongshan Hospital, Xiamen University, Xiamen, Fujian, China
| | - Mei-Zhu Hong
- Department of Traditional Chinese Medicine, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Jin-Shui Pan
- Department of Hepatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
- Hepatology Research Institute, Fujian Medical University, Fuzhou, Fujian, China.
- Department of Hepatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hosptial, Fujian Medical University, Fuzhou, Fujian, China.
- Fujian Clinical Research Center for Hepatopathy and Intestinal Diseases, Fuzhou, Fujian, China.
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Li M, Shi Y, Zhao J, Wang Q, Li M, Zhao X. Identification of potential susceptibility genes in patients with primary Sjögren's syndrome-associated pulmonary arterial hypertension through whole exome sequencing. Arthritis Res Ther 2023; 25:175. [PMID: 37730603 PMCID: PMC10510152 DOI: 10.1186/s13075-023-03171-y] [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: 05/05/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a rare complication of primary Sjögren's syndrome (pSS). Several genes have proven to be associated with pSS and PAH. However, there is no study specifically addressing the genetic susceptibility in pSS combined with PAH. METHODS Thirty-four unrelated patients with pSS-PAH were recruited from April 2019 to July 2021 at Peking Union Medical College Hospital. Demographic and clinical data were recorded in detail, and peripheral blood samples were collected for whole-exome sequencing (WES). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to predict the functional effect of mutant genes. Genetic variants identified by WES were confirmed by polymerase chain reaction (PCR)-Sanger sequencing. RESULTS We totally identified 141 pathogenic variant loci of 129 genes in these 34 pSS-PAH patients, using WES analysis. Patients with a family history of rheumatic diseases are more likely to carry FLG mutations or carry gene variations related to the biosynthesis of the amino acids pathway (p < 0.05). According to Sanger sequencing confirmation and pathogenicity validation, we totally identified five candidate pathogenic variants including FLG c.12064A > T, BCR c.3275_3278dupCCGG, GIGYF2 c.3463C > A, ITK c.1741C > T, and SLC26A4 c.919-2A > G. CONCLUSION Our findings provide preliminary data of exome sequencing to identify susceptibility loci for pSS-PAH and enriched our understanding of the genetic etiology for pSS-PAH. The candidate pathogenic genes may be the potential genetic markers for early warning of this disease.
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Affiliation(s)
- Mucong Li
- Department of Medical Genetics, Institute of Basic Medical Sciences & Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Rheumatology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Chinese Rheumatism Data Center (CRDC), Chinese SLE Treatment and Research Group (CSTAR), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yue Shi
- Department of Medical Genetics, Institute of Basic Medical Sciences & Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Rheumatology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Chinese Rheumatism Data Center (CRDC), Chinese SLE Treatment and Research Group (CSTAR), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Chinese Rheumatism Data Center (CRDC), Chinese SLE Treatment and Research Group (CSTAR), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Qian Wang
- Department of Rheumatology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Chinese Rheumatism Data Center (CRDC), Chinese SLE Treatment and Research Group (CSTAR), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Mengtao Li
- Department of Rheumatology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Chinese Rheumatism Data Center (CRDC), Chinese SLE Treatment and Research Group (CSTAR), State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Xiuli Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences & Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China.
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [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: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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6
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He Y, Chen Y, Yao L, Wang J, Sha X, Wang Y. The Inflamm-Aging Model Identifies Key Risk Factors in Atherosclerosis. Front Genet 2022; 13:865827. [PMID: 35706446 PMCID: PMC9191626 DOI: 10.3389/fgene.2022.865827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Atherosclerosis, one of the main threats to human life and health, is driven by abnormal inflammation (i.e., chronic inflammation or oxidative stress) during accelerated aging. Many studies have shown that inflamm-aging exerts a significant impact on the occurrence of atherosclerosis, particularly by inducing an immune homeostasis imbalance. However, the potential mechanism by which inflamm-aging induces atherosclerosis needs to be studied more thoroughly, and there is currently a lack of powerful prediction models.Methods: First, an improved inflamm-aging prediction model was constructed by integrating aging, inflammation, and disease markers with the help of machine learning methods; then, inflamm-aging scores were calculated. In addition, the causal relationship between aging and disease was identified using Mendelian randomization. A series of risk factors were also identified by causal analysis, sensitivity analysis, and network analysis.Results: Our results revealed an accelerated inflamm-aging pattern in atherosclerosis and suggested a causal relationship between inflamm-aging and atherosclerosis. Mechanisms involving inflammation, nutritional balance, vascular homeostasis, and oxidative stress were found to be driving factors of atherosclerosis in the context of inflamm-aging.Conclusion: In summary, we developed a model integrating crucial risk factors in inflamm-aging and atherosclerosis. Our computation pipeline could be used to explore potential mechanisms of related diseases.
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Affiliation(s)
- Yudan He
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yao Chen
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Lilin Yao
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Junyi Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Xianzheng Sha
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Yin Wang,
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Harley IT, 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] [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 (HI3), 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,Corresponding author at: Isaac TW Harley, MD, PhD, MS, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Barbara Davis Center, Mail Stop B115, 1775 Aurora Court, Aurora, CO 80045, USA, (I.T.W. Harley)
| | - 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,Corresponding author at: Amr H. Sawalha, MD, University of Pittsburgh, 7123 Rangos Research Center, 4401 Penn Avenue, Pittsburgh, PA 15224, USA, (A.H. Sawalha)
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8
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Hagemeijer YP, Guryev V, Horvatovich P. Accurate Prediction of Protein Sequences for Proteogenomics Data Integration. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:233-260. [PMID: 34905178 DOI: 10.1007/978-1-0716-1936-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This book chapter discusses proteogenomics data integration and provides an overview into the different omics layer involved in defining the proteome of a living organism. Various aspects of genome variability affecting either the sequence or abundance level of proteins are discussed in this book chapter, such as the effect of single-nucleotide variants or larger genomic structural variants on the proteome. Next, various sequencing technologies are introduced and discussed from a proteogenomics data integration perspective such as those providing short- and long-read sequencing and listing their respective advantages and shortcomings for accurate protein variant prediction using genomic/transcriptomics sequencing data. Finally, the various bioinformatics tools used to process and analyze DNA/RNA sequencing data are discussed with the ultimate goal of obtaining accurately predicted sample-specific protein sequences that can be used as a drop-in replacement in existing approaches for peptide and protein identification using popular database search engines such as MSFragger, SearchGUI/PeptideShaker.
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Affiliation(s)
- Yanick Paco Hagemeijer
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands.
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9
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Qi X, Wang XQ, Jin L, Gao LX, Guo HF. Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren's syndrome. Bioengineered 2021; 12:9313-9331. [PMID: 34723755 PMCID: PMC8809958 DOI: 10.1080/21655979.2021.2000245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Primary Sjogren’s syndrome (pSS) is a complex systemic autoimmune disease, which is difficult to accurately diagnose due to symptom diversity in patients, especially at earlier stages. We tried to find potential single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and related signaling pathways. Genomic DNA was extracted from peripheral blood of 12 individuals (7 individuals from 3 pSS pedigrees and 5 sporadic cases) for whole-exome sequencing (WES) analysis. SNPs and CNVs were identified, followed by functional annotation of genes with SNPs and CNVs. Gene expression profile (involving 64 normal controls and 166 cases) was downloaded from the Gene Expression Omnibus database (GEO) dataset for differentially expression analysis. Sanger sequencing and in vitro validation was used to validate the identified SNPs and differentially expressed genes, respectively. A total of 5 SNPs were identified in both pedigrees and sporadic cases, such as FES, PPM1J, and TRAPPC9. A total of 3402 and 19 CNVs were identified in pedigrees and sporadic cases, respectively. Fifty-one differentially expressed genes were associated with immunity, such as BATF3, LAP3, BATF2, PARP9, and IL15RA. AMPK signaling pathway and cell adhesion molecules (CAMs) were the most significantly enriched signaling pathways of identified SNPs. Identified CNVs were associated with systemic lupus erythematosus, mineral absorption, and HTLV-I infection. IL2-STAT5 signaling, interferon-gamma response, and interferon-alpha response were significantly enriched immune related signaling pathways of identified differentially expressed genes. In conclusion, our study found some potential SNPs, CNVs, and related signaling pathways, which could be useful in understanding the pathological mechanism of pSS.
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Affiliation(s)
- Xuan Qi
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xi-Qin Wang
- Internal Medicine, Yuhua Yunfang Integrated Traditional Chinese and Western Medicine Clinic, Shijiazhuang, Hebei, China
| | - Lu Jin
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Li-Xia Gao
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Hui-Fang Guo
- Department of Rheumatism and Immunology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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10
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Maluf SW, Wilhelm Filho D, Parisotto EB, Medeiros GDSD, Pereira CHJ, Maraslis FT, Dornelles Schoeller CC, Rosa JSD, Fröde TS. DNA damage, oxidative stress, and inflammation in children with celiac disease. Genet Mol Biol 2020; 43:e20180390. [PMID: 32555942 PMCID: PMC7288666 DOI: 10.1590/1678-4685-gmb-2018-0390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
The objective of this study was to evaluate the level of genomic instability in patients with celiac disease and to establish a relationship between inflammation, oxidative stress, and DNA damage in these patients. Myeloperoxidase (MPO) activity, adenosine deaminase, nitric oxide (NOx), thiobarbituric acid, catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and DNA damage were evaluated in peripheral blood samples from 47 celiac disease patients and 31 controls. Patients with celiac disease presented higher levels of DNA damage in comparison to controls (p=0.023). This difference was also observed for markers of oxidative stress, such as CAT (p=0.011) and SOD (p=0.013), and inflammatory markers such as MPO (p < 0.001) and NOx (p=0.009). Positive correlations were found between DNA damage levels and the values of CAT (r=0.405; p=0.009) and SOD (r=0.516; p < 0.001). Positive correlations were also found between GPx and NOx (r=0.349; p=0.030) and MPO and NOx (r=0.239; p=0.039). CAT and NOx showed a negative correlation (r= −0.315; p=0.042). In conclusion, intestinal inflammation can have systemic effects, causing an imbalance between oxidant and antioxidant markers, which may promote increased levels of DNA damage.
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Affiliation(s)
- Sharbel Weidner Maluf
- Universidade Federal de Santa Catarina, Hospital Universitário, Laboratório de Genética, Florianópolis, SC, Brazil
| | - Danilo Wilhelm Filho
- Universidade Federal de Santa Catarina, Departamento de Ecologia e Zoologia, Florianópolis, SC, Brazil
| | - Eduardo Benedetti Parisotto
- Universidade Federal de Mato Grosso do Sul, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Campo Grande, MS, Brazil
| | | | | | - Flora Troina Maraslis
- Universidade Federal de Santa Catarina, Hospital Universitário, Laboratório de Genética, Florianópolis, SC, Brazil
| | | | - Julia Savan da Rosa
- Universidade Federal de Santa Catarina, Centro de Ciências de Saúde, Departamento de Análises Clínicas, Florianópolis, SC, Brazil
| | - Tânia Silvia Fröde
- Universidade Federal de Santa Catarina, Centro de Ciências de Saúde, Departamento de Análises Clínicas, Florianópolis, SC, Brazil
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11
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Meyerson W, Leisman J, Navarro FCP, Gerstein M. Origins and characterization of variants shared between databases of somatic and germline human mutations. BMC Bioinformatics 2020; 21:227. [PMID: 32498674 PMCID: PMC7273669 DOI: 10.1186/s12859-020-3508-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/20/2020] [Indexed: 01/26/2023] Open
Abstract
Background Mutations arise in the human genome in two major settings: the germline and the soma. These settings involve different inheritance patterns, time scales, chromatin structures, and environmental exposures, all of which impact the resulting distribution of substitutions. Nonetheless, many of the same single nucleotide variants (SNVs) are shared between germline and somatic mutation databases, such as between the gnomAD database of 120,000 germline exomes and the TCGA database of 10,000 somatic exomes. Here, we sought to explain this overlap. Results After strict filtering to exclude common germline polymorphisms and sites with poor coverage or mappability, we found 336,987 variants shared between the somatic and germline databases. A uniform statistical model explains 34% of these shared variants; a model that incorporates the varying mutation rates of the basic mutation types explains another 50% of shared variants; and a model that includes extended nucleotide contexts (e.g. surrounding 3 bases on either side) explains an additional 4% of shared variants. Analysis of read depth finds mixed evidence that up to 4% of the shared variants may represent germline variants leaked into somatic call sets. 9% of the shared variants are not explained by any model. Sequencing errors and convergent evolution did not account for these. We surveyed other factors as well: Cancers driven by endogenous mutational processes share a greater fraction of variants with the germline, and recently derived germline variants were more likely to be somatically shared than were ancient germline ones. Conclusions Overall, we find that shared variants largely represent bona fide biological occurrences of the same variant in the germline and somatic setting and arise primarily because DNA has some of the same basic chemical vulnerabilities in either setting. Moreover, we find mixed evidence that somatic call-sets leak appreciable numbers of germline variants, which is relevant to genomic privacy regulations. In future studies, the similar chemical vulnerability of DNA between the somatic and germline settings might be used to help identify disease-related genes by guiding the development of background-mutation models that are informed by both somatic and germline patterns of variation.
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Affiliation(s)
- William Meyerson
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Yale School of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - John Leisman
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06510, USA
| | - Fabio C P Navarro
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA.,Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Mark Gerstein
- Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Yale School of Medicine, Yale University, New Haven, CT, 06510, USA. .,Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA. .,Department of Computer Science, Yale University, New Haven, CT, 06511, USA.
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12
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Somatic mTOR mutation in clonally expanded T lymphocytes associated with chronic graft versus host disease. Nat Commun 2020; 11:2246. [PMID: 32382059 PMCID: PMC7206083 DOI: 10.1038/s41467-020-16115-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: 08/12/2019] [Accepted: 04/13/2020] [Indexed: 12/16/2022] Open
Abstract
Graft versus host disease (GvHD) is the main complication of allogeneic hematopoietic stem cell transplantation (HSCT). Here we report studies of a patient with chronic GvHD (cGvHD) carrying persistent CD4+ T cell clonal expansion harboring somatic mTOR, NFKB2, and TLR2 mutations. In the screening cohort (n = 134), we detect the mTOR P2229R kinase domain mutation in two additional cGvHD patients, but not in healthy or HSCT patients without cGvHD. Functional analyses of the mTOR mutation indicate a gain-of-function alteration and activation of both mTORC1 and mTORC2 signaling pathways, leading to increased cell proliferation and decreased apoptosis. Single-cell RNA sequencing and real-time impedance measurements support increased cytotoxicity of mutated CD4+ T cells. High throughput drug-sensitivity testing suggests that mutations induce resistance to mTOR inhibitors, but increase sensitivity for HSP90 inhibitors. Our findings imply that somatic mutations may contribute to aberrant T cell proliferations and persistent immune activation in cGvHD, thereby paving the way for targeted therapies. Chronic graft versus host disease (cGvHD) is a major cause of morbidity and mortality in allogeneic bone marrow transplantation. Here the authors identify a recurrent activating mTOR mutation in expanded donor T-cell clones of 3 cGvHD patients, which suggests somatic mutations may contribute to GvHD pathogenesis and opens avenues to targeted therapies.
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13
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Kabadi A, McDonnell E, Frank CL, Drowley L. Applications of Functional Genomics for Drug Discovery. SLAS DISCOVERY 2020; 25:823-842. [PMID: 32026742 DOI: 10.1177/2472555220902092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many diseases, such as diabetes, autoimmune diseases, cancer, and neurological disorders, are caused by a dysregulation of a complex interplay of genes. Genome-wide association studies have identified thousands of disease-linked polymorphisms in the human population. However, detailing the causative gene expression or functional changes underlying those associations has been elusive in many cases. Functional genomics is an emerging field of research that aims to deconvolute the link between genotype and phenotype by making use of large -omic data sets and next-generation gene and epigenome editing tools to perturb genes of interest. Here we review how functional genomic tools can be used to better understand the biological interplay between genes, improve disease modeling, and identify novel drug targets. Incorporation of functional genomic capabilities into conventional drug development pipelines is predicted to expedite the development of first-in-class therapeutics.
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Affiliation(s)
- Ami Kabadi
- Element Genomics, a UCB company, Durham, NC, USA
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14
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Sabbadin C, Ceccato F, Ragazzi E, Boscaro M, Betterle C, Armanini D. Evaluation of angiotensin II type-1 receptor antibodies in primary aldosteronism and further considerations about their possible pathogenetic role. J Clin Hypertens (Greenwich) 2018; 20:1313-1318. [PMID: 30058103 DOI: 10.1111/jch.13351] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/09/2018] [Accepted: 06/16/2018] [Indexed: 12/18/2022]
Abstract
Angiotensin II type-1 receptor autoantibodies (AT1RAb) have been involved in the genesis of primary aldosteronism (PA), both in aldosterone-producing adenoma (APA) and in idiopathic hyperaldosteronism (IHA). In this study, we evaluated the titer of AT1RAb in 44 PA patients (15 with APA and 29 with IHA) compared with 18 normotensive healthy controls who were matched for gender and age. In 17 PA patients (6 APA and 11 IHA) the titer was evaluated under mineralocorticoid receptor (MR) antagonist treatment. We found that PA patients had a significantly higher titer of AT1RAb compared with controls (median values 33 [IQR 15.6] IU/mL vs 17.5 [IQR 10.8] IU/mL, respectively; P < 0.0001). No significant difference of the AT1RAb titer was reported among PA patients, subdivided according to the subtypes and the concomitant MR antagonist therapy. No significant correlation was detected between age, gender, BMI, blood pressure values, baseline aldosterone, ARR, and the AT1RAb titer of all patients enrolled. Our data confirm an increased titer of AT1RAb in both subtypes of PA, independently from the concomitant use of MR antagonists and clinical/biochemical characteristics of PA patients. The small sample of patients and the relatively short time of treatment could have influenced these results. Moreover, the ELISA assay fails to evaluate the bioactivity of AT1RAb. Further studies should evaluate if the subtype, the clinical/biochemical recovery of PA, or both, influence the pathogenetic role of AT1RAb. The possible autoimmune pathogenesis and reversal effect with AT1R blocker treatment in PA patients with AT1RAb positivity is intriguing and requires further study.
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Affiliation(s)
- Chiara Sabbadin
- Department of Medicine, Endocrinology, University of Padova, Padova, Italy
| | - Filippo Ceccato
- Department of Medicine, Endocrinology, University of Padova, Padova, Italy
| | - Eugenio Ragazzi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Marco Boscaro
- Department of Medicine, Endocrinology, University of Padova, Padova, Italy
| | - Corrado Betterle
- Department of Medicine, Endocrinology, University of Padova, Padova, Italy
| | - Decio Armanini
- Department of Medicine, Endocrinology, University of Padova, Padova, Italy
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15
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Genetic contributions to lupus nephritis in a multi-ethnic cohort of systemic lupus erythematous patients. PLoS One 2018; 13:e0199003. [PMID: 29953444 PMCID: PMC6023154 DOI: 10.1371/journal.pone.0199003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/30/2018] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE African Americans, East Asians, and Hispanics with systemic lupus erythematous (SLE) are more likely to develop lupus nephritis (LN) than are SLE patients of European descent. The etiology of this difference is not clear, and this study was undertaken to investigate how genetic variants might explain this effect. METHODS In this cross-sectional study, 1244 SLE patients from multiethnic case collections were genotyped for 817,810 single-nucleotide polymorphisms (SNPs) across the genome. Continental genetic ancestry was estimated utilizing the program ADMIXTURE. Gene-based testing and pathway analysis was performed within each ethnic group and meta-analyzed across ethnicities. We also performed candidate SNP association tests with SNPs previously established as risk alleles for SLE, LN, and chronic kidney disease (CKD). Association testing and logistic regression models were performed with LN as the outcome, adjusted for continental ancestries, sex, disease duration, and age. RESULTS We studied 255 North European, 263 South European, 238 Hispanic, 224 African American and 264 East Asian SLE patients, of whom 606 had LN (48.7%). In genome-wide gene-based and candidate SNP analyses, we found distinct genes, pathways and established risk SNPs associated with LN for each ethnic group. Gene-based analyses showed significant associations between variation in ZNF546 (p = 1.0E-06), TRIM15 (p = 1.0E-06), and TRIMI0 (p = 1.0E-06) and LN among South Europeans, and TTC34 (p = 8.0E-06) was significantly associated with LN among Hispanics. The SNP rs8091180 in NFATC1 was associated with LN (OR 1.43, p = 3.3E-04) in the candidate SNP meta-analysis with the highest OR among African-Americans (OR 2.17, p = 0.0035). CONCLUSION Distinct genetic factors are associated with the risk of LN in SLE patients of different ethnicities. CKD risk alleles may play a role in the development of LN in addition to SLE-associated risk variants. These findings may further explain the clinical heterogeneity of LN risk and response to therapy observed between different ethnic groups.
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16
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Hussain MS, Tripathi V. Smoking under hypoxic conditions: a potent environmental risk factor for inflammatory and autoimmune diseases. Mil Med Res 2018; 5:11. [PMID: 29598831 PMCID: PMC5877397 DOI: 10.1186/s40779-018-0158-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Autoimmune disease management presents a significant challenge to medical science. Environmental factors potentially increase the risk of developing inflammatory and autoimmune diseases, such as multiple sclerosis, rheumatoid arthritis, and lupus. Among various environmental stresses, cigarette smoke and hypoxia have both been reported to lead to an enhanced risk of inflammatory and autoimmune diseases.In this review, we shed light on all reported mechanisms whereby cigarette smoke and a hypoxic environment can induce inflammatory and autoimmune diseases and discuss how hypoxic conditions influence the cigarette smoke-induced threat of inflammatory and autoimmune disease development.Cigarette smoke and hypoxia both lead to increased oxidative stress and production of reactive oxygen species and other free radicals, which have various effects including the generation of autoreactive pro-inflammatory T cells and autoantibodies, reductions in T regulatory (Treg) cell activity, and enhanced expression of pro-inflammatory mediators [e.g., interleukin-6 (IL-6), interleukin-4 (IL-4) and interleukin-8 (IL-8)]. Accordingly, smoking and hypoxic environments may synergistically act as potent environmental risk factors for inflammatory and autoimmune diseases. To our knowledge, no studies have reported the direct association of cigarette smoke and hypoxic environments with the risk of developing inflammatory and autoimmune diseases.Future studies exploring the risk of autoimmune disease development in smokers at high altitudes, particularly military personnel and mountaineers who are not acclimatized to high-altitude regions, are required to obtain a better understanding of disease risk as well as its management.
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Affiliation(s)
- Md. Saddam Hussain
- School of Biotechnology, Gautam Buddha University, Greater Noida, Gautam Budh Nagar, Uttar Pradesh 201312 India
| | - Vishwas Tripathi
- School of Biotechnology, Gautam Buddha University, Greater Noida, Gautam Budh Nagar, Uttar Pradesh 201312 India
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17
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Stojković V, Fujimori DG. Mutations in RNA methylating enzymes in disease. Curr Opin Chem Biol 2017; 41:20-27. [PMID: 29059606 DOI: 10.1016/j.cbpa.2017.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 01/06/2023]
Abstract
RNA methylation is an abundant modification identified in various RNA species in both prokaryotic and eukaryotic organisms. However, the functional roles for the majority of these methylations remain largely unclear. In eukaryotes, many RNA methylations have been suggested to participate in fundamental cellular processes. Mutations in eukaryotic RNA methylating enzymes, and a consequent change in methylation, can lead to the development of diseases and disorders. In contrast, loss of RNA methylation in prokaryotes can be beneficial to microorganisms, especially under antibiotic pressure. Here we discuss several recent advances in understanding mutational landscape of both eukaryotic and prokaryotic RNA methylating enzymes and their relevance to disease and antibiotic resistance.
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Affiliation(s)
- Vanja Stojković
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States.
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18
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Tavakolpour S. Towards personalized medicine for patients with autoimmune diseases: Opportunities and challenges. Immunol Lett 2017; 190:130-138. [DOI: 10.1016/j.imlet.2017.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/03/2017] [Indexed: 02/06/2023]
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19
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Stefano GB, Bjenning C, Wang F, Wang N, Kream RM. Mitochondrial Heteroplasmy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 982:577-594. [PMID: 28551808 DOI: 10.1007/978-3-319-55330-6_30] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic polymorphisms, in concert with well-characterized etiology and progression of major pathologies, plays a significant role in aberrant processes afflicting human populations. Mitochondrial heteroplasmy represents a dynamically determined co-expression of inherited polymorphisms and somatic pathology in varying ratios within individual mitochondrial DNA (mtDNA) genomes with repetitive patterns of tissue specificity. The ratios of the MtDNA genomes represent a balance between healthy and pathological cellular outcomes. Mechanistically, cardiomyopathies have profound alterations of normative mitochondrial function. Certain allele imbalances in the nuclear mitochondrial genome are associated with key energy mitochondrial proteins. Mitochondrial heteroplasmy may manifest itself at critical protein expression points, e.g., cytochrome c oxidase (COX). Pathological mtDNA mutations also are associated with the development of congestive heart failure. Interestingly, mitochondrial 'normal vs. abnormal' ratios of various heteroplasmic populations may occur in families. In the translational context of human health and disease, we discuss the need for determining critical foci to probe multiple biological roles of mitochondrial heteroplasmy in cardiomyopathy.
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Affiliation(s)
- George B Stefano
- International Scientific Information, Inc., 150 Broadhollow Rd, Ste 114, Melville, NY, 11747, USA.
| | - Christina Bjenning
- Cardiometabolic Designs LLC, 160 W15th Ave, Suite 303, Sea Cliff, NY, 11579, USA
| | - Fuzhou Wang
- Division of Neuroscience, Bonoi Academy of Science & Education, Chapel Hill, NC, 27510, USA
| | - Nan Wang
- Department of Anesthesiology, Affiliated Hospital of OB/GYN, Nanjing Medical University, Nanjing, 210004, China
| | - Richard M Kream
- International Scientific Information, Inc., 150 Broadhollow Rd, Ste 114, Melville, NY, 11747, USA
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20
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Armanini D, Andrisani A, Donà G, Bordin L, Ambrosini G, Sabbadin C. Hypothesis on a relationship between hyperaldosteronism, inflammation, somatic mutations, and autoimmunity. J Clin Hypertens (Greenwich) 2017; 19:1060-1062. [DOI: 10.1111/jch.13074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Decio Armanini
- Department of Medicine, Endocrinology (DIMED); University of Padua; Padua Italy
| | | | - Gabriella Donà
- Department of Medicine, Endocrinology (DIMED); University of Padua; Padua Italy
| | - Luciana Bordin
- Department of Molecular Medicine, Biological Chemistry; University of Padua; Padua Italy
| | - Guido Ambrosini
- Department of Women's Health, Salus Pueri; University of Padua; Padua Italy
| | - Chiara Sabbadin
- Department of Medicine, Endocrinology (DIMED); University of Padua; Padua Italy
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21
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Stefano GB, Kream RM. Mitochondrial DNA heteroplasmy in human health and disease. Biomed Rep 2016; 4:259-262. [PMID: 26998260 PMCID: PMC4774312 DOI: 10.3892/br.2016.590] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/02/2016] [Indexed: 12/14/2022] Open
Abstract
The biomedical literature has extensively documented the functional roles of genetic polymorphisms in concert with well-characterized somatic mutations in the etiology and progression of major metastatic diseases afflicting human populations. Mitochondrial heteroplasmy exists as a dynamically determined co-expression of inherited polymorphisms and somatic mutations in varying ratios within individual mitochondrial DNA genomes with repetitive patterns of tissue specificity. Mechanistically, carcinogenic cellular processes include profound alterations of normative mitochondrial function, notably dependence on aerobic and anaerobic glycolysis, and aberrant production and release of lactate, according to a classic theory. Within the translational context of human health and disease, the present review discusses the necessity of establishing critical foci designed to probe multiple biological roles of mitochondrial heteroplasmy in cancer biology.
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Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM, Rheinbay E, Kim J, Maruvka YE, Braunstein LZ, Kamburov A, Hanawalt PC, Wheeler DA, Koren A, Lawrence MS, Getz G. Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell 2016; 164:538-49. [PMID: 26806129 DOI: 10.1016/j.cell.2015.12.050] [Citation(s) in RCA: 288] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/21/2015] [Accepted: 12/24/2015] [Indexed: 12/20/2022]
Abstract
Mutational processes constantly shape the somatic genome, leading to immunity, aging, cancer, and other diseases. When cancer is the outcome, we are afforded a glimpse into these processes by the clonal expansion of the malignant cell. Here, we characterize a less explored layer of the mutational landscape of cancer: mutational asymmetries between the two DNA strands. Analyzing whole-genome sequences of 590 tumors from 14 different cancer types, we reveal widespread asymmetries across mutagenic processes, with transcriptional ("T-class") asymmetry dominating UV-, smoking-, and liver-cancer-associated mutations and replicative ("R-class") asymmetry dominating POLE-, APOBEC-, and MSI-associated mutations. We report a striking phenomenon of transcription-coupled damage (TCD) on the non-transcribed DNA strand and provide evidence that APOBEC mutagenesis occurs on the lagging-strand template during DNA replication. As more genomes are sequenced, studying and classifying their asymmetries will illuminate the underlying biological mechanisms of DNA damage and repair.
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Affiliation(s)
- Nicholas J Haradhvala
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Paz Polak
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Petar Stojanov
- Carnegie Mellon University School of Computer Science, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Kyle R Covington
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Eve Shinbrot
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Julian M Hess
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Esther Rheinbay
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jaegil Kim
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Yosef E Maruvka
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Lior Z Braunstein
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Atanas Kamburov
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Philip C Hanawalt
- Stanford University Department of Biology, 450 Serra Mall, Stanford, CA 94305, USA
| | - David A Wheeler
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Amnon Koren
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Cornell University Department of Molecular Biology and Genetics, 526 Campus Road, Ithaca, NY 14853, USA
| | - Michael S Lawrence
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Department of Pathology, 55 Fruit Street, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
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Genomic Copy Number Variation Affecting Genes Involved in the Cell Cycle Pathway: Implications for Somatic Mosaicism. Int J Genomics 2015; 2015:757680. [PMID: 26421275 PMCID: PMC4569762 DOI: 10.1155/2015/757680] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/27/2015] [Indexed: 12/20/2022] Open
Abstract
Somatic genome variations (mosaicism) seem to represent a common mechanism for human intercellular/interindividual diversity in health and disease. However, origins and mechanisms of somatic mosaicism remain a matter of conjecture. Recently, it has been hypothesized that zygotic genomic variation naturally occurring in humans is likely to predispose to nonheritable genetic changes (aneuploidy) acquired during the lifetime through affecting cell cycle regulation, genome stability maintenance, and related pathways. Here, we have evaluated genomic copy number variation (CNV) in genes implicated in the cell cycle pathway (according to Kyoto Encyclopedia of Genes and Genomes/KEGG) within a cohort of patients with intellectual disability, autism, and/or epilepsy, in which the phenotype was not associated with genomic rearrangements altering this pathway. Benign CNVs affecting 20 genes of the cell cycle pathway were detected in 161 out of 255 patients (71.6%). Among them, 62 individuals exhibited >2 CNVs affecting the cell cycle pathway. Taking into account the number of individuals demonstrating CNV of these genes, a support for this hypothesis appears to be presented. Accordingly, we speculate that further studies of CNV burden across the genes implicated in related pathways might clarify whether zygotic genomic variation generates somatic mosaicism in health and disease.
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