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Elendu C, Amaechi DC, Elendu TC, Ozigis MO, Adegbola MO, Adebayo MA, Afolabi OG. Renal disease associated with multiple sclerosis: A narrative review. Medicine (Baltimore) 2024; 103:e38222. [PMID: 38758897 PMCID: PMC11098179 DOI: 10.1097/md.0000000000038222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/14/2024] [Indexed: 05/19/2024] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurological disorder characterized by central nervous system demyelination, leading to various neurological impairments. While the primary focus of research and clinical management has centered on the neurological aspects of MS, emerging evidence suggests a complex interplay between MS and renal disease. This narrative review endeavors to elucidate the intriguing association between MS and renal disease, providing a comprehensive overview of the current knowledge on this topic. Our review begins by outlining the pathophysiology of MS and the diverse mechanisms contributing to its progression. We then delve into renal disease, categorizing the various types and their clinical presentations. This review focuses on exploring the intricate relationship between these seemingly distinct conditions. We analyze existing literature to uncover shared risk factors, potential pathophysiological links, and the impact of MS on renal function. Furthermore, we discuss the clinical presentation and diagnostic challenges in identifying renal disease in MS patients. Importantly, we examine available treatment options and their efficacy in managing renal complications in this unique patient population. The consequences of renal disease on the overall quality of life (QOL) for individuals living with MS are also examined, shedding light on the multifaceted burden of these coexisting conditions.
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Breitwieser GE, Cippitelli A, Wang Y, Pelletier O, Dershem R, Wei J, Toll L, Fakhoury B, Brunori G, Metpally R, Carey DJ, Robishaw J. Rare GPR37L1 Variants Reveal Potential Association between GPR37L1 and Disorders of Anxiety and Migraine. J Neurosci 2024; 44:e1226232024. [PMID: 38569927 PMCID: PMC11089846 DOI: 10.1523/jneurosci.1226-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
GPR37L1 is an orphan receptor that couples through heterotrimeric G-proteins to regulate physiological functions. Since its role in humans is not fully defined, we used an unbiased computational approach to assess the clinical significance of rare G-protein-coupled receptor 37-like 1 (GPR37L1) genetic variants found among 51,289 whole-exome sequences from the DiscovEHR cohort. Rare GPR37L1 coding variants were binned according to predicted pathogenicity and analyzed by sequence kernel association testing to reveal significant associations with disease diagnostic codes for epilepsy and migraine, among others. Since associations do not prove causality, rare GPR37L1 variants were functionally analyzed in SK-N-MC cells to evaluate potential signaling differences and pathogenicity. Notably, receptor variants exhibited varying abilities to reduce cAMP levels, activate mitogen-activated protein kinase (MAPK) signaling, and/or upregulate receptor expression in response to the agonist prosaptide (TX14(A)), as compared with the wild-type receptor. In addition to signaling changes, knock-out (KO) of GPR37L1 or expression of certain rare variants altered cellular cholesterol levels, which were also acutely regulated by administration of the agonist TX14(A) via activation of the MAPK pathway. Finally, to simulate the impact of rare nonsense variants found in the large patient cohort, a KO mouse line lacking Gpr37l1 was generated. Although KO animals did not recapitulate an acute migraine phenotype, the loss of this receptor produced sex-specific changes in anxiety-related disorders often seen in chronic migraineurs. Collectively, these observations define the existence of rare GPR37L1 variants associated with neuropsychiatric conditions in the human population and identify the signaling changes contributing to pathological processes.
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Affiliation(s)
- Gerda E Breitwieser
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Andrea Cippitelli
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Yingcai Wang
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Oliver Pelletier
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Ridge Dershem
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Jianning Wei
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Lawrence Toll
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Bianca Fakhoury
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | - Gloria Brunori
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
| | | | - David J Carey
- Geisinger, Weis Center for Research, Danville, Pennsylvania
| | - Janet Robishaw
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida
- College of Veterinary Medicine, University of Florida, Gainesville, Florida
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Taeubert MJ, Kuipers TB, Zhou J, Li C, Wang S, Wang T, Tobi EW, Belsky DW, Lumey LH, Heijmans BT. Adults prenatally exposed to the Dutch Famine exhibit a metabolic signature associated with a broad spectrum of common diseases. medRxiv 2024:2024.04.04.24305284. [PMID: 38633796 PMCID: PMC11023671 DOI: 10.1101/2024.04.04.24305284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Background Exposure to famine in the prenatal period is associated with an increased risk of metabolic disease, including obesity and type-2 diabetes. We employed nuclear magnetic resonance (NMR) metabolomic profiling to provide a deeper insight into the metabolic changes associated with survival of prenatal famine exposure during the Dutch Famine at the end of World War II and explore their link to disease. Methods NMR metabolomics data were generated from serum in 480 individuals prenatally exposed to famine (mean 58.8 years, 0.5 SD) and 464 controls (mean 57.9 years, 5.4 SD). We tested associations of prenatal famine exposure with levels of 168 individual metabolic biomarkers and compared the metabolic biomarker signature of famine exposure with those of 154 common diseases. Results Prenatal famine exposure was associated with higher concentrations of branched-chain amino acids ((iso)-leucine), aromatic amino acid (tyrosine), and glucose in later life (0.2-0.3 SD, p < 3x10-3). The metabolic biomarker signature of prenatal famine exposure was positively correlated to that of incident type-2 diabetes (r = 0.77, p = 3x10-27), also when re-estimating the signature of prenatal famine exposure among individuals without diabetes (r = 0.67, p = 1x10-18). Remarkably, this association extended to 115 common diseases for which signatures were available (0.3 ≤ r ≤ 0.9, p < 3.2x10-4). Correlations among metabolic signatures of famine exposure and disease outcomes were attenuated when the famine signature was adjusted for body mass index. Conclusions Prenatal famine exposure is associated with a metabolic biomarker signature that strongly resembles signatures of a diverse set of diseases, an observation that can in part be attributed to a shared involvement of obesity.
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Affiliation(s)
- M. Jazmin Taeubert
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas B. Kuipers
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Jiayi Zhou
- Butler Columbia Aging Center, Columbia University, New York, United States
| | - Chihua Li
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, United States
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, United States
| | - Tian Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, United States
| | - Elmar W. Tobi
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Daniel W. Belsky
- Butler Columbia Aging Center, Columbia University, New York, United States
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, United States
| | - L. H. Lumey
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, United States
| | - Bastiaan T. Heijmans
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
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Noble JA, Besançon S, Sidibé AT, Rozemuller EH, Rijkers M, Dadkhodaie F, de Bruin H, Kooij J, Martin HRN, Ogle GD, Mack SJ. Complete HLA genotyping of type 1 diabetes patients and controls from Mali reveals both expected and novel disease associations. HLA 2024; 103:e15319. [PMID: 38226399 PMCID: PMC10863981 DOI: 10.1111/tan.15319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024]
Abstract
HLA genotyping was performed on 99 type 1 diabetes (T1D) patients and 200 controls from Mali. Next-generation sequencing of the classical HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1 loci revealed strong T1D association for all loci except HLA-C and -DPA1. Class II association is stronger than class I association, with most observed associations predisposing or protective as expected based on previous studies. For example, HLA-DRB1*03:01, HLA-DRB1*09:01, and HLA-DRB1*04:05 predispose for T1D, whereas HLA-DRB1*15:03 is protective. HLA-DPB1*04:02 (OR = 12.73, p = 2.92 × 10-05 ) and HLA-B*27:05 (OR = 21.36, p = 3.72 × 10-05 ) appear highly predisposing, although previous studies involving multiple populations have reported HLA-DPB1*04:02 as T1D-protective and HLA-B*27:05 as neutral. This result may reflect the linkage disequilibrium between alleles on the extended HLA-A*24:02~HLA-B*27:05~HLA-C*02:02~HLA-DRB1*04:05~HLA-DRB4*01:03~HLA-DQB1*02:02~HLA-DQA1*02:01~HLA-DPB1*04:02~HLA-DPA1*01:03 haplotype in this population rather than an effect of either allele itself. Individual amino acid (AA) analyses are consistent with most T1D association attributable to HLA class II rather than class I in this data set. AA-level analyses reveal previously undescribed differences of the HLA-C locus from the HLA-A and HLA-B loci, with more polymorphic positions, spanning a larger portion of the gene. This may reflect additional mechanisms for HLA-C to influence T1D risk, for example, through expression differences or through its role as the dominant ligand for killer cell immunoglobulin-like receptors (KIR). Comparison of these data to those from larger studies and on other populations may facilitate T1D prediction and help elucidate elusive mechanisms of how HLA contributes to T1D risk and autoimmunity.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, California, USA
- Department of Pediatrics, University of California, San Francisco, Oakland, California, USA
| | | | | | | | | | | | | | | | - Harper R N Martin
- Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Graham D Ogle
- Life for a Child Program, Diabetes Australia, Glebe, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Steven J Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, California, USA
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Sullivan HC, Gandhi MJ, Gaitonde S, Narasimhan R, Gendzekhadze K, Pandey S, Roby RK, Maha GC, Kaur H, Schiller JJ, McDowell J, Smith M, Liu C, Morris GP. Seventy-five years of service: an overview of the College of American Pathologists' proficiency testing program in histocompatibility and identity testing. Front Genet 2023; 14:1331169. [PMID: 38169613 PMCID: PMC10758433 DOI: 10.3389/fgene.2023.1331169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
The Histocompatibility and Identity Testing Committee offers an overview of the College of American Pathologists' (CAP) Proficiency Testing (PT) program, commemorating its significant 75th anniversary in 2024. The CAP PT program has undergone significant growth and evolution over the years, ultimately achieving Centers for Medicare and Medicaid Services approval. In 1979, CAP's partnership with the American Association for Clinical Histocompatibility Testing marked a pivotal moment, leading to the creation of the first proficiency testing survey in 1980. This laid the foundation for various PT programs managed by the CAP Histocompatibility and Identity Testing Committee, including HLA antibody testing, HLA molecular typing, engraftment monitoring, parentage/relationship testing, HLA disease associations and drug risk, and HLA-B27 typing. Each program's distinctive considerations, grading methodologies, and future prospects are detailed here, highlighting the continual evolution of histocompatibility and identity testing PT to support emerging technologies and evolving laboratory practices in the field.
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Affiliation(s)
- H. Cliff Sullivan
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Manish J. Gandhi
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, United States
| | - Sujata Gaitonde
- Department of Pathology, University of Illinois Chicago, Chicago, IL, United States
| | - Ramya Narasimhan
- Boston University Medical Center, Department of Pathology and Laboratory Medicine, Boston, MA, United States
| | | | - Soumya Pandey
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Rhonda K. Roby
- Alameda County Sheriff’s Office Crime Laboratory, Oakland, CA, United States
| | | | - Harmeet Kaur
- Cuyahoga County Regional Forensic Science Lab, Cleveland, OH, United States
| | | | - Julie McDowell
- College of American Pathologist (CAP), Chicago, IL, United States
| | - Maria Smith
- College of American Pathologist (CAP), Chicago, IL, United States
| | - Chang Liu
- Washington University in St. Louis, Department of Pathology and Immunology, Saint Louis, MO, United States
| | - Gerald P. Morris
- Department of Pathology, Univeristy of California San Diego, San Diego, CA, United States
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Mrazek F. Population genetics and external proficiency testing for HLA disease associations. Front Genet 2023; 14:1268705. [PMID: 37937194 PMCID: PMC10626483 DOI: 10.3389/fgene.2023.1268705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023] Open
Abstract
Numerous associations of HLA variants with susceptibility to diseases, namely, those with an immunopathological component, have been described to date. The strongest HLA associations were incorporated into the standard algorithms for the diagnostics. Disease-associated HLA variants are routinely detected by various techniques including DNA-based assays. For the identification of HLA markers or their combinations with the highest diagnostic value and those with frequent clinical indications (e.g., HLA-B*27, -B*57:01, -DQ2/-DQ8, -DQB1*06:02), diagnostic tests that focus on a single or limited number of specific HLA antigens/alleles, have already been developed; the use of complete typing for particular HLA loci is a relevant alternative. Importantly, external proficiency testing (EPT) became an integral part of good laboratory practice for HLA disease associations in accredited laboratories and not only supports correct "technical" identification of the associated HLA variants, but also adequate interpretation of the results to the clinicians. In the present article selected aspects of EPT for HLA disease associations related to population genetics are reviewed and discussed with the emphasis on the optimal level of HLA typing resolution, population-based differences in disease associated HLA alleles within the allelic group, distribution and linkage disequilibrium of HLA alleles in particular populations and interpretation of the presence of less common HLA variants/haplotypes. In conclusion, the laboratories that perform and interpret the tests to the clinicians, producers of the certified diagnostics and EPT providers should consider, among others, the genetic characteristics of the populations in order to optimise the diagnostic value of the tests for disease-associated HLA variants.
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Affiliation(s)
- Frantisek Mrazek
- HLA laboratory, Department of Immunology, University Hospital, Olomouc, Czechia
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Mohanraj U, Konttinen T, Salava A, Väkevä L, Ranki A, Söderlund-Venermo M. Significant Association of Cutavirus With Parapsoriasis en Plaques: High Prevalence Both in Skin Swab and Biopsy Samples. Clin Infect Dis 2023; 77:987-990. [PMID: 37234048 PMCID: PMC10552579 DOI: 10.1093/cid/ciad320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/24/2023] [Indexed: 05/27/2023] Open
Abstract
Cutavirus (CuV) is associated with cutaneous T-cell lymphoma (CTCL), of which parapsoriasis is a precursor. Our study reveals a significantly higher CuV-DNA prevalence in skin swabs of parapsoriasis patients (6/13; 46.2%) versus those of healthy adults (1/51; 1.96%). Eight patients (8/12; 66.7%) had CuV DNA in biopsied skin, and 4 developed CTCL.
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Affiliation(s)
| | - Tuomas Konttinen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alexander Salava
- Department of Dermatology, Allergology, and Venereology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Liisa Väkevä
- Department of Dermatology, Allergology, and Venereology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Annamari Ranki
- Department of Dermatology, Allergology, and Venereology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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8
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Zheng H, Yang J, Feng Y, Duan H, Du L, Shu Q, Li H. Systematic exploration of eczema-associated paediatric diseases in a Chinese population of millions: A retrospective observation study. Clin Transl Allergy 2023; 13:e12249. [PMID: 37227416 DOI: 10.1002/clt2.12249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Eczema is the most common form of dermatitis and also the starting point of atopic march. Although many eczema-associated allergic and immunologic disorders have been studied, there remains a gap in the systematic quantitative knowledge regarding the relationships between all childhood disorders and eczema. This study aimed to systematically explore eczema-associated childhood diseases using a real-world, long-term clinical dataset generated from millions of children in China. METHODS Data were collected at 8,907,735 outpatient healthcare visits from 2,592,147 children between January 1, 2013, and August 15, 2019, at the largest comprehensive pediatric medical center in Zhejiang Province of China. The period prevalence differences in various pediatric diseases between children with and without eczema were used to test the independence of various pediatric disorders and eczema using Fisher's exact test. Bonferroni correction was used to adjust the p value in multiple testing. Odds ratio >2 with 95% confidence interval not including 1 and adjusted p < 0.05 was used to identify eczema-associated diseases. RESULTS Overall, 234 pediatric disorders were identified from more than 6000 different pediatric disorders. An interactive eczema-associated disease map that has related quantitative epidemiological features called ADmap was published at http://pedmap.nbscn.org/admap. Thirty-six of these disease associations have not been reported in previous studies. CONCLUSION This systematic exploratory study confirmed the associations of many well-known diseases with eczema in Chinese children and also identified some novel and interesting associations. These results are valuable for the development of a comprehensive approach to the management of eczema in childhood.
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Affiliation(s)
- Huiwen Zheng
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jian Yang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Yuqing Feng
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Huilong Duan
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Lizhong Du
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Qiang Shu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Haomin Li
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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9
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Wang H, Ho C. The Human Pre-miRNA Distance Distribution for Exploring Disease Association. Int J Mol Sci 2023; 24:ijms24021009. [PMID: 36674554 PMCID: PMC9862702 DOI: 10.3390/ijms24021009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs), playing an important role in cell differentiation, development, gene regulation, and apoptosis, have attracted much attention in recent years. miRNAs were shown to be involved in the mechanisms of various diseases, and certainly, they can be employed as useful disease biomarkers. The phylogenetic tree analysis of miRNA biomarkers is a useful tool to investigate the association between various diseases as well as the association between viruses and disease. In addition to the phylogenetic tree analysis, a more advanced study is to use the miRNA distance distribution to evaluate the similarity of the miRNA biomarkers. The mature miRNA distance distribution based on mature miRNA sequences has been derived. The averages of the pairwise distances of miRNA biomarkers for several associated diseases were shown to be smaller than the overall mean of all miRNAs, which indicates the high similarity of miRNA biomarkers for associated diseases. In addition to the mature miRNA, the precursor miRNA (pre-miRNA) may be more useful to explore the similarity of miRNAs because the mature miRNA duplex is released from the pre-miRNA. Therefore, in this study, the distance distributions based on human pre-miRNA stem-loop sequences were derived. The 1917 human miRNA stem-loop sequences in the miRBase dataset were used to derive the pre-miRNA distance distribution, and this is the first study to provide the distance distribution based on the human pre-miRNAs. The similarity of miRNA biomarkers for several associated diseases or vaccines was examined using the derived distribution, and the results show that the similarity of pre-miRNA biomarkers may be a feasible way to help explore the disease association.
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10
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Ohnuki Y, Suzuki S, Uruha A, Oyama M, Suzuki S, Kulski JK, Nishino I, Shiina T. Association of immune-mediated necrotizing myopathy with HLA polymorphisms. HLA 2022; 101:449-457. [PMID: 36565042 DOI: 10.1111/tan.14950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022]
Abstract
Immune-mediated necrotizing myopathy (IMNM) is a type of autoimmune myositis typically characterized clinically by proximal muscle weakness with elevated creatine kinase levels, pathologically by myofiber necrosis and regeneration with paucity of lymphocytic cell infiltration, and serologically by the presence of either of two myositis-specific autoantibodies, anti-SRP, and anti-HMGCR antibodies. However, the HLA loci and alleles associated with IMNM are still not fully understood at least partly because IMNM was a relatively recently established condition. In this study, we genotyped the six HLA loci (HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1) in 250 patients (237 patients over age 18 years and 13 juvenile patients) diagnosed with IMNM based on clinicopathological features and autoantibody information and performed a case control study with Japanese healthy subjects. In the adult patients, specific HLA alleles associated with IMNM were identified at all HLA loci, with DRB1*08:03 showing the strongest association (OR = 2.5; p = 0.00000017). Furthermore, subgroup analysis with various clinical information showed that C*03:04 (OR = 3.7; p = 0.00012) was a higher risk allele for collagen disease in adult patients, and B*13:01 (OR = 23.2; p = 0.021) and C*03:04 (OR = 5.8; p = 0.0074) were higher risk for juvenile patients with anti-HMGCR antibody-positive IMNM. These findings will help to better understand the HLA genetic background and features of IMNM in designing future studies.
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Affiliation(s)
- Yuko Ohnuki
- Department of Medical Ethics, Tokai University School of Medicine, Kanagawa, Japan.,Department of Clinical Genetics, Tokai University Hospital, Kanagawa, Japan
| | - Shigeaki Suzuki
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Akinori Uruha
- Department of Neuromuscular Research, National Institute of Neuroscience, and Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Neurology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Munenori Oyama
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, and Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
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11
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Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM, Ulirsch J, Everett S, Howrigan DP, Boone PM, Fu J, Karczewski KJ, Kellaris G, Lowther C, Lucente D, Mohajeri K, Nõukas M, Nuttle X, Samocha KE, Trinh M, Ullah F, Võsa U, Hurles ME, Aradhya S, Davis EE, Finucane H, Gusella JF, Janze A, Katsanis N, Matyakhina L, Neale BM, Sanders D, Warren S, Hodge JC, Lal D, Ruderfer DM, Meck J, Mägi R, Esko T, Reymond A, Kutalik Z, Hakonarson H, Sunyaev S, Brand H, Talkowski ME. A cross-disorder dosage sensitivity map of the human genome. Cell 2022; 185:3041-3055.e25. [PMID: 35917817 PMCID: PMC9742861 DOI: 10.1016/j.cell.2022.06.036] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023]
Abstract
Rare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. In this study, we aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome. We harmonized and meta-analyzed rCNVs from nearly one million individuals to construct a genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage sensitive segments associated with at least one disorder. These segments were typically gene dense and often harbored dominant dosage sensitive driver genes, which we were able to prioritize using statistical fine-mapping. Finally, we designed an ensemble machine-learning model to predict probabilities of dosage sensitivity (pHaplo & pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 triplosensitive genes, including 648 that were uniquely triplosensitive. This dosage sensitivity resource will provide broad utility for human disease research and clinical genetics.
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Affiliation(s)
- Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eleonora Porcu
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Maarja Lepamets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | | | | | - Lide Han
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Theodore Morley
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Jacob Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Selin Everett
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Daniel P Howrigan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Konrad J Karczewski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Georgios Kellaris
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Margit Nõukas
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Xander Nuttle
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kaitlin E Samocha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | - Mi Trinh
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | - Farid Ullah
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | | | | | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10, UK
| | | | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hilary Finucane
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | | | - Nicholas Katsanis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Lurie Children's Hospital, Chicago, IL 60611, USA; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Benjamin M Neale
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, 51149 Cologne, Germany; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Precision Medicine, Department of Biomedical Informatics, and Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for Primary Care and Public Health, University of Lausanne, 1015 Lausanne, Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shamil Sunyaev
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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12
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Sharma M, Jha IP, Chawla S, Pandey N, Chandra O, Mishra S, Kumar V. Associating pathways with diseases using single-cell expression profiles and making inferences about potential drugs. Brief Bioinform 2022; 23:6623725. [PMID: 35772850 DOI: 10.1093/bib/bbac241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
Finding direct dependencies between genetic pathways and diseases has been the target of multiple studies as it has many applications. However, due to cellular heterogeneity and limitations of the number of samples for bulk expression profiles, such studies have faced hurdles in the past. Here, we propose a method to perform single-cell expression-based inference of association between pathway, disease and cell-type (sci-PDC), which can help to understand their cause and effect and guide precision therapy. Our approach highlighted reliable relationships between a few diseases and pathways. Using the example of diabetes, we have demonstrated how sci-PDC helps in tracking variation of association between pathways and diseases with changes in age and species. The variation in pathways-disease associations in mice and humans revealed critical facts about the suitability of the mouse model for a few pathways in the context of diabetes. The coherence between results from our method and previous reports, including information about the drug target pathways, highlights its reliability for multidimensional utility.
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Affiliation(s)
- Madhu Sharma
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Indra Prakash Jha
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Smriti Chawla
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Neetesh Pandey
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Omkar Chandra
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Shreya Mishra
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
| | - Vibhor Kumar
- Department of computational biology, Indraprastha Institute of Information Technology, Okhla Ph-III, New Delhi
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13
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Delwart E, Tisza MJ, Altan E, Li Y, Deng X, Hartigan-O'Connor DJ, Ardeshir A. Idiopathic Chronic Diarrhea in Rhesus Macaques Is Not Associated with Enteric Viral Infections. Viruses 2021; 13:2503. [PMID: 34960771 DOI: 10.3390/v13122503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/26/2021] [Accepted: 12/08/2021] [Indexed: 11/18/2022] Open
Abstract
While recent changes in treatment have reduced the lethality of idiopathic chronic diarrhea (ICD), this condition remains one of the most common causes of rhesus macaque deaths in non-human primate research centers. We compared the viromes in fecal swabs from 52 animals with late stage ICD and 41 healthy animals. Viral metagenomics targeting virus-like particles was used to identify viruses fecally shed by each animal. Five viruses belonging to the Picornaviridae, one to the Caliciviridae, one to the Parvoviridae, and one to the Adenoviridae families were identified. The fraction of reads matching each viral species was then used to estimate and compare viral loads in ICD cases versus healthy controls. None of the viruses detected in fecal swabs were strongly associated with ICD.
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14
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Wickramasinghe LC, van Wijngaarden P, Tsantikos E, Hibbs ML. The immunological link between neonatal lung and eye disease. Clin Transl Immunology 2021; 10:e1322. [PMID: 34466225 PMCID: PMC8387470 DOI: 10.1002/cti2.1322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/02/2021] [Accepted: 07/13/2021] [Indexed: 01/02/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) and retinopathy of prematurity (ROP) are two neonatal diseases of major clinical importance, arising in large part as a consequence of supplemental oxygen therapy used to promote the survival of preterm infants. The presence of coincident inflammation in the lungs and eyes of neonates receiving oxygen therapy indicates that a dysregulated immune response serves as a potential common pathogenic factor for both diseases. This review examines the current state of knowledge of immunological dysregulation in BPD and ROP, identifying similarities in the cellular subsets and inflammatory cytokines that are found in the alveoli and retina during the active phase of these diseases, indicating possible mechanistic overlap. In addition, we highlight gaps in the understanding of whether these responses emerge independently in the lung and retina as a consequence of oxygen exposure or arise because of inflammatory spill‐over from the lung. As BPD and ROP are anatomically distinct, they are often considered discreet disease entities and are therefore treated separately. We propose that an improved understanding of the relationship between BPD and ROP is key to the identification of novel therapeutic targets to treat or prevent both conditions simultaneously.
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Affiliation(s)
- Lakshanie C Wickramasinghe
- Leukocyte Signalling LaboratoryDepartment of Immunology and PathologyCentral Clinical SchoolMonash UniversityMelbourneVICAustralia
| | - Peter van Wijngaarden
- OphthalmologyDepartment of SurgeryUniversity of MelbourneMelbourneVICAustralia
- Centre for Eye Research AustraliaRoyal Victorian Eye and Ear HospitalEast MelbourneVICAustralia
| | - Evelyn Tsantikos
- Leukocyte Signalling LaboratoryDepartment of Immunology and PathologyCentral Clinical SchoolMonash UniversityMelbourneVICAustralia
| | - Margaret L Hibbs
- Leukocyte Signalling LaboratoryDepartment of Immunology and PathologyCentral Clinical SchoolMonash UniversityMelbourneVICAustralia
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15
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Schindler E, Dribus M, Duffy BF, Hock K, Farnsworth CW, Gragert L, Liu C. HLA genetic polymorphism in patients with Coronavirus Disease 2019 in Midwestern United States. HLA 2021; 98:370-379. [PMID: 34338446 PMCID: PMC8429120 DOI: 10.1111/tan.14387] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022]
Abstract
The experience of individuals with Coronavirus Disease 2019 (COVID‐19) ranges from asymptomatic to life threatening multi‐organ dysfunction. Specific HLA alleles may affect the predisposition to severe COVID‐19 because of their role in presenting viral peptides to launch the adaptive immune response to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). In this population‐based case–control study in the midwestern United States, we performed high‐resolution HLA typing of 234 cases hospitalized for COVID‐19 in the St. Louis metropolitan area and compared their HLA allele frequencies with those of 22,000 matched controls from the National Marrow Donor Program (NMDP). We identified two predisposing alleles, HLA‐DRB1*08:02 in the Hispanic group (OR = 9.0, 95% confidence interval: 2.2–37.9; adjusted p = 0.03) and HLA‐A*30:02 in younger African Americans with ages below the median (OR = 2.2, 1.4–3.6; adjusted p = 0.01), and several candidate alleles with potential associations with COVID‐19 in African American, White, and Hispanic groups. We also detected risk‐associated amino acid residues in the peptide binding grooves of some of these alleles, suggesting the presence of functional associations. These findings support the notion that specific HLA alleles may be protective or predisposing factors to COVID‐19. Future consortium analysis of pooled cases and controls is warranted to validate and extend these findings, and correlation with viral peptide binding studies will provide additional evidence for the functional association between HLA alleles and COVID‐19.
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Affiliation(s)
- Emily Schindler
- Department of Laboratory Medicine, Mercy Hospital, St. Louis, Missouri, USA
| | - Marian Dribus
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Brian F Duffy
- HLA Laboratory, Barnes-Jewish Hospital, St. Louis, Missouri, USA
| | - Karl Hock
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher W Farnsworth
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Loren Gragert
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Chang Liu
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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16
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Profaizer T, Dibb K, Bethers H, Monds C, Andreasen J, Delgado JC, Lázár-Molnár E. Comparison of Next-Generation Sequencing-Based Human Leukocyte Antigen Typing with Clinical Flow Cytometry and Allele-Specific PCR Melting Assays for HLA-B27 Genotyping. J Appl Lab Med 2021; 6:1221-1227. [PMID: 34151972 DOI: 10.1093/jalm/jfab046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Due to the strong association between ankylosing spondylitis and Human Leukocyte Antigen (HLA)-B27, accurate identification of HLA-B27 is important in the diagnosis of patients with suspected spondyloarthritides. For this study, we compared a high-resolution HLA-B typing method to the clinical flow cytometry and allele-specific PCR melting assays to determine clinical benefits of high-resolution testing. METHODS Residual clinical samples submitted for HLA-B27 testing by flow cytometry were tested by single-locus HLA-B genotyping using next-generation sequencing (NGS), and PCR with melting curve analysis, currently used as a reflex test for indeterminate flow cytometry results. RESULTS Fifty out of the 51 samples (98%) positive by flow cytometry confirmed as HLA-B27 positive by PCR melting assay and by NGS. The sample that did not confirm was genotyped as HLA-B*07:02. All the samples negative by flow cytometry were confirmed as HLA-B27 negative by both PCR melting assay and NGS. For the group that was indeterminate by flow cytometry, 84.5% (n = 49) typed as positive for HLA-B27, while 15.5% (n = 9) were negative for HLA-B27 but positive for HLA-B*07:02. NGS was the only method able to distinguish between pathogenic and nonpathogenic HLA-B27 variants, in contrast to the flow cytometry or the PCR melting assays. CONCLUSIONS Single-locus NGS is superior to flow cytometry and PCR melting assay for the unambiguous identification of HLA-B27 variants, and uniquely able to distinguish between pathogenic and nonpathogenic B27 alleles. Due to its high accuracy, it may be a feasible superior alternative to flow cytometry and traditional molecular methods for clinical HLA-B27 testing.
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Affiliation(s)
- Tracie Profaizer
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - Kimberly Dibb
- Histocompatibility & Immunogenetics Laboratory, University of Utah Health, Salt Lake City, UT
| | - Holly Bethers
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - Cassandra Monds
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - John Andreasen
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - Julio C Delgado
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Eszter Lázár-Molnár
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
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17
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Liu TW, Wu YR, Chen YC, Fung HC, Chen CM. Polymorphisms of Interleukin-6 and Interleukin-8 Are Not Associated with Parkinson's Disease in Taiwan. Brain Sci 2021; 11:brainsci11060768. [PMID: 34207646 PMCID: PMC8229237 DOI: 10.3390/brainsci11060768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 11/06/2022] Open
Abstract
Background: Studies have suggested that cytokines are crucial mediators in the pathogenesis of Parkinson’s disease (PD). The multifunctional cytokine interleukin (IL)-6 and its single nucleotide polymorphisms (SNPs) were found to have an impact on the development of PD. However, different studies in associations of IL-6 genetic variants with PD showed inconsistent results and it has never been explored in a Taiwanese population. Both IL-1α and IL-8 contribute to the same inflammation pathway. IL-1α genetic polymorphism has an effect on late-onset PD in Taiwan, whereas the associations of IL-8 genetic variants with PD in Taiwan remain to be investigated. Methods: This study examined the frequencies of polymorphisms within the critical promoter areas of the proinflammatory cytokine genes: IL-6 G-174C (rs1800795) and IL-8 A-251T (rs4073) in Taiwanese PD patients compared with age-and gender-matched healthy subjects. Comparisons were also made in genotype and allele frequencies of IL-6 G-174C (rs1800795) and IL-8 A-251T (rs4073) among different populations in previous studies. Results: In total, 1120 subjects, including 509 PD patients (female/male: 259/250) and 511 control subjects (female/male: 252/259), were recruited. We found no statistically significant differences in IL-6 G-174C (rs1800795) or IL-8 A-251T (rs4073) genotypic and allelic distribution between PD and controls, even after being stratified by age at onset and gender. Conclusions: The results did not demonstrate any association of IL-6 G-174C (rs1800795) or IL-8 A-251T (rs4073) with PD in a Taiwanese population. Despite the negative results, this is the first study in associations of IL-6 G-174C (rs1800795) and IL-8 A-251T (rs4073) with PD in Taiwan. The relevance of genetic variants of IL-6 G-174C (rs1800795) or IL-8 A-251T (rs4073) on PD susceptibility warrants further investigation.
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Affiliation(s)
- Tsai-Wei Liu
- Department of Neurology, Chang-Gung Memorial Hospital, 5 Fuhsing St., Gueishan, Tauoyan 333, Taiwan; (T.-W.L.); (Y.-R.W.); (Y.-C.C.)
| | - Yih-Ru Wu
- Department of Neurology, Chang-Gung Memorial Hospital, 5 Fuhsing St., Gueishan, Tauoyan 333, Taiwan; (T.-W.L.); (Y.-R.W.); (Y.-C.C.)
- Department of Neurology, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1st Rd., Kwei-Shan Dist, Tauoyan 333, Taiwan
| | - Yi-Chun Chen
- Department of Neurology, Chang-Gung Memorial Hospital, 5 Fuhsing St., Gueishan, Tauoyan 333, Taiwan; (T.-W.L.); (Y.-R.W.); (Y.-C.C.)
- Department of Neurology, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1st Rd., Kwei-Shan Dist, Tauoyan 333, Taiwan
| | - Hon-Chung Fung
- Fu Jen Faculty of Theology of St. Robert Bellarmine, Fu Jen University Clinic, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 242, Taiwan;
| | - Chiung-Mei Chen
- Department of Neurology, Chang-Gung Memorial Hospital, 5 Fuhsing St., Gueishan, Tauoyan 333, Taiwan; (T.-W.L.); (Y.-R.W.); (Y.-C.C.)
- Department of Neurology, College of Medicine, Chang-Gung University, 259 Wen-Hwa 1st Rd., Kwei-Shan Dist, Tauoyan 333, Taiwan
- Correspondence: ; Tel.: +886-3-3281200 (ext. 8729); Fax: +886-3-3227226
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18
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Prakash S, Shukla S, Bhagat AK, Mishra H, Vangala R, Jain A. Human parvovirus 4: An emerging etiological agent in cases presenting with influenza like illness. J Med Virol 2021; 93:5158-5162. [PMID: 33017052 DOI: 10.1002/jmv.26579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 08/22/2020] [Accepted: 09/14/2020] [Indexed: 11/12/2022]
Abstract
This study was planned to study the association of parvovirus 4 (PARV4) with Influenza-like illness (ILI). A total of 1111 patients with a clinical diagnosis of ILI and 220 healthy controls were tested for Influenza A/HINI/and H3N2, Influenza B, and PARV4. Further sequencing was done to analyze the genotype distribution of parvovirus 4. Influenza A/HINI, A/H3N2, and B were detected in 334 (30.06%), 9 (0.81%), and 10 (0.9%) cases respectively. PARV4 was detected in 135 (12.15%) cases and one healthy control. Parvovirus 4 was significantly higher in cases as compared to controls (relative risk, 30.77%; p < .0006). Sequencing of 20 isolates suggests the dominance of genotype 2 in our region.
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Affiliation(s)
- Shantanu Prakash
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Suruchi Shukla
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Amit K Bhagat
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Hricha Mishra
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Ramakrishna Vangala
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
| | - Amita Jain
- Department of Microbiology, King Georges Medical University, Lucknow, UP, India
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19
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de Weerd NA, Vivian JP, Lim SS, Huang SUS, Hertzog PJ. Structural integrity with functional plasticity: what type I IFN receptor polymorphisms reveal. J Leukoc Biol 2021; 108:909-924. [PMID: 33448473 DOI: 10.1002/jlb.2mr0420-152r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 03/21/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
The type I IFNs activate an array of signaling pathways, which are initiated after IFNs bind their cognate receptors, IFNα/β receptor (IFNAR)1 and IFNAR2. These signals contribute to many aspects of human health including defense against pathogens, cancer immunosurveillance, and regulation of inflammation. How these cytokines interact with their receptors influences the quality of these signals. As such, the integrity of receptor structure is pivotal to maintaining human health and the response to immune stimuli. This review brings together genome wide association studies and clinical reports describing the association of nonsynonymous IFNAR1 and IFNAR2 polymorphisms with clinical disease, including altered susceptibility to viral and bacterial pathogens, autoimmune diseases, cancer, and adverse reactions to live-attenuated vaccines. We describe the amino acid substitutions or truncations induced by these polymorphisms and, using the knowledge of IFNAR conformational changes, IFNAR-IFN interfaces and overall structure-function relationship of the signaling complexes, we hypothesize the effect of these polymorphisms on receptor structure. That these predicted changes to IFNAR structure are associated with clinical manifestations of human disease, highlights the importance of IFNAR structural integrity to maintaining functional quality of these receptor-mediated responses. Type I IFNs are pivotal to innate immune responses and ultimately, to human health. Understanding the consequences of altered structure on the actions of these clinically significant cell receptors provides important information on the roles of IFNARs in health and disease.
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Affiliation(s)
- Nicole A de Weerd
- Centre for Innate Immunity and Infectious Diseases, Department of Molecular and Translational Science, Hudson Institute of Medical Research and Monash University, Clayton, Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute and Australian Research Council Centre for Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - San S Lim
- Centre for Innate Immunity and Infectious Diseases, Department of Molecular and Translational Science, Hudson Institute of Medical Research and Monash University, Clayton, Victoria, Australia
| | - Stephanie U-Shane Huang
- Centre for Innate Immunity and Infectious Diseases, Department of Molecular and Translational Science, Hudson Institute of Medical Research and Monash University, Clayton, Victoria, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Department of Molecular and Translational Science, Hudson Institute of Medical Research and Monash University, Clayton, Victoria, Australia
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20
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Li H, Cvejic E, Gu B, Vollmer-Conna U, Hickie I, Wakefield D, Davenport T, Wiley J, Lloyd AR. Regulation of the Acute Sickness Response by the P2RX7 Receptor. J Infect Dis 2021; 224:914-920. [PMID: 33471105 DOI: 10.1093/infdis/jiab027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The acute sickness response to infection is a stereotyped set of illness manifestations initiated by proinflammatory signals in the periphery but mediated centrally. P2RX7 is a highly polymorphic gene encoding an ATP-gated cationic pore, widely expressed on immune cells and the brain, and regulating the NLRP3 inflammasome, as well as diverse neural functions. METHODS Associations between P2RX7 genotype, pore activity, and illness manifestations were examined in a cohort with acute viral and bacterial infections (n = 484). Genotyping of 12 P2RX7 function-modifying single-nucleotide polymorphisms (SNPs) was used to identify haplotypes and diplotypes. Leucocyte pore activity was measured by uptake of the fluorescent dye, YO-PRO-1, and by ATP-induced interleukin-1β (IL-1β) release. Associations were sought with scores describing the symptom domains, or endophenotypes, derived from principal components analysis. RESULTS Among the 12 SNPs, a 4-SNP haplotype block with 5 variants was found in 99.5% of the subjects. These haplotypes and diplotypes were closely associated with variations in pore activity and IL-1β production. Homozygous diplotypes were associated with overall illness severity as well as fatigue, pain, and mood disturbances. CONCLUSIONS P2RX7 signaling plays a significant role in the acute sickness response to infection, likely acting in both the immune system and the brain.
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Affiliation(s)
- Hui Li
- Viral Immunology Systems Program, Kirby Institute, University of New South Wales, Sydney, Australia
| | - Erin Cvejic
- Department of Human Behaviour, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Ben Gu
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Ute Vollmer-Conna
- Department of Human Behaviour, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Ian Hickie
- Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - Denis Wakefield
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | | | - James Wiley
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew R Lloyd
- Viral Immunology Systems Program, Kirby Institute, University of New South Wales, Sydney, Australia
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21
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Anukul N, Pathanapitoon K, Leetrakool N, Guntiya T, Wita R, Palacajornsuk P, Klangsinsirikul P. HLA-DRB1*04:05 and HLA-DQB1*04:01: Alleles Potentially Associated with Vogt-Koyanagi-Harada in Northern Thai Patients. Ocul Immunol Inflamm 2020; 29:260-263. [PMID: 32965138 DOI: 10.1080/09273948.2020.1813315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE To determine the frequency and association of alleles at human leukocyte antigen (HLA)-DRB1 and HLA-DQB1 loci in VKH disease patients from Northern Thailand. METHODS A case-control study was conducted with three subject groups: 23 VKH patients, 20 patients with other uveitis entities, and 40 healthy blood donors. HLA-DRB1 and HLA-DQB1 loci were analyzed and the frequency of HLA-DRB1 and HLA-DQB1 alleles was calculated by direct counting. The measure of association was calculated by odds ratio (OR) and 95% confidence interval. RESULTS In VKH patients, the most prevalent allele was HLA-DRB1*04:05, found in 35% of patients and with the highest OR (42.13). HLA-DQB1*04:01 was the next most prevalent, found in 23.91% of VKH patients. HLA-DQB1*05:02 was also detected in 23.91% of patients; however, a higher prevalence was observed in non-VKH and healthy controls (30% and 35%, respectively). CONCLUSION HLA-DRB1*04:05 and HLA-DQB1*04:01 could be potential genetic markers for VKH.
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Affiliation(s)
- Nampeung Anukul
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Kessara Pathanapitoon
- Department of Ophthalmology, Faculty of Medicines, Chiang Mai University, Chiang Mai, Thailand
| | - Nipapan Leetrakool
- Blood Bank Section, Maharaj Nakorn Chiang Mai Hospital, Faculty of Medicines, Chiang Mai University, Chiang Mai, Thailand
| | - Tiphakorn Guntiya
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Ratsameetip Wita
- Department of Computer Science, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Poonsub Palacajornsuk
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Phennapha Klangsinsirikul
- Division of Transfusion Science, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
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22
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Väisänen E, Fu Y, Koskenmies S, Fyhrquist N, Wang Y, Keinonen A, Mäkisalo H, Väkevä L, Pitkänen S, Ranki A, Hedman K, Söderlund-Venermo M. Cutavirus DNA in Malignant and Nonmalignant Skin of Cutaneous T-Cell Lymphoma and Organ Transplant Patients but Not of Healthy Adults. Clin Infect Dis 2020; 68:1904-1910. [PMID: 30239652 DOI: 10.1093/cid/ciy806] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/14/2018] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Three new parvoviruses of Protoparvovirus genus, bufavirus (BuV), tusavirus (TuV), and cutavirus (CuV), have recently been discovered in diarrheal stools. CuV was further detected in a proportion of cutaneous T-cell lymphoma (CTCL)/mycosis fungoides skin samples and in one melanoma. PATIENTS AND METHODS With novel multiplex quantitative polymerase chain reaction and antibody assays, we studied 3 patient groups for BuV, TuV, and CuV DNA and immunoglobulin G (IgG): CTCL patients, immunosuppressed solid-organ transplant recipients, and immunocompetent healthy adults. RESULTS CuV DNA was detected in skin biopsies of 4/25 (16.0%) CTCL and 4/136 (2.9%) transplant patients but not in any of 159 skin samples of 98 healthy adults. The dermal CuV-DNA prevalence was significantly higher in CTCL patients than in the other subjects. CuV DNA was further detected in healthy skin of 4 organ transplant recipients, 2 of whom also had CuV-positive skin carcinomas. One CTCL patient harbored CuV DNA in both malignant (CTCL, melanoma) and nonmalignant skin and sentinel lymph nodes but not in his prostate. The CuV IgG seroprevalences were among CTCL patients 9.5% (4/42), transplant recipients 6.5% (8/124), and healthy adults 3.8% (3/78). BuV and TuV DNAs were absent and antibodies infrequent in all cohorts. Parvoviral antibodies were shown to persist for ≥20 years and dermal CuV DNA for 4 years. All 3 CuV-DNA-positive patients, with both biopsies and sera available, were CuV-IgG positive. CONCLUSION Our results suggest that dermal CuV DNA carriage is associated with CTCL. Any putative roles of CuV in the carcinogenesis must be determined in forthcoming studies.
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Affiliation(s)
| | - Yu Fu
- Department of Virology, University of Helsinki, Finland
| | - Sari Koskenmies
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Central Hospital, Finland
| | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Bacteriology and Immunology, University of Helsinki, Finland
| | - Yilin Wang
- Department of Virology, University of Helsinki, Finland
| | - Anne Keinonen
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Central Hospital, Finland
| | | | - Liisa Väkevä
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Central Hospital, Finland
| | - Sari Pitkänen
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Central Hospital, Finland
| | - Annamari Ranki
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Central Hospital, Finland
| | - Klaus Hedman
- Department of Virology, University of Helsinki, Finland
- Helsinki University Hospital, Finland
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23
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Abstract
Intron retention (IR) is an alternative splicing mode whereby introns, rather than being spliced out as usual, are retained in mature mRNAs. It was previously considered a consequence of mis-splicing and received very limited attention. Only recently has IR become of interest for transcriptomic data analysis owing to its recognized roles in gene expression regulation and associations with complex diseases. In this article, we first review the function of IR in regulating gene expression in a number of biological processes, such as neuron differentiation and activation of CD4+ T cells. Next, we briefly review its association with diseases, such as Alzheimer's disease and cancers. Then, we describe state-of-the-art methods for IR detection, including RNA-seq analysis tools IRFinder and iREAD, highlighting their underlying principles and discussing their advantages and limitations. Finally, we discuss the challenges for IR detection and potential ways in which IR detection methods could be improved.
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Affiliation(s)
- Jian-Tao Zheng
- Hunan Provincial Key Lab on Bioinformatics, Center for Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Cui-Xiang Lin
- Hunan Provincial Key Lab on Bioinformatics, Center for Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Zhao-Yu Fang
- School of Mathematics and Statistics, Central South University, Changsha, China
| | - Hong-Dong Li
- Hunan Provincial Key Lab on Bioinformatics, Center for Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
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24
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Poulton K, Wright P, Hughes P, Savic S, Welberry Smith M, Guiver M, Morton M, van Dellen D, Tholouli E, Wynn R, Clark B. A role for human leucocyte antigens in the susceptibility to SARS-Cov-2 infection observed in transplant patients. Int J Immunogenet 2020; 47:324-328. [PMID: 32623831 PMCID: PMC7361549 DOI: 10.1111/iji.12505] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/04/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023]
Abstract
We analysed data from 80 patients who tested positive for SARS‐CoV‐2 RNA who had previously been HLA typed to support transplantation. Data were combined from two adjacent centres in Manchester and Leeds to achieve a sufficient number for early analysis. HLA frequencies observed were compared against two control populations: first, against published frequencies in a UK deceased donor population (n = 10,000) representing the target population of the virus, and second, using a cohort of individuals from the combined transplant waiting lists of both centres (n = 308), representing a comparator group of unaffected individuals of the same demographic. We report a significant HLA association with HLA‐ DQB1*06 (53% vs. 36%; p < .012; OR 1.96; 95% CI 1.94–3.22) and infection. A bias towards an increased representation of HLA‐A*26, HLA‐DRB1*15, HLA‐DRB1*10 and DRB1*11 was also noted but these were either only significant using the UK donor controls, or did not remain significant after correction for multiple tests. Likewise, HLA‐A*02, HLA‐B*44 and HLA‐C*05 may exert a protective effect, but these associations did not remain significant after correction for multiple tests. This is relevant information for the clinical management of patients in the setting of the current SARS‐CoV‐2 pandemic and potentially in risk‐assessing staff interactions with infected patients.
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Affiliation(s)
- Kay Poulton
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester, UK.,Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Paul Wright
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester, UK
| | - Pamela Hughes
- Transplant Immunology, St James's University Hospital, Leeds, UK
| | - Sinisa Savic
- Department Immunology, St James's University Hospital, Leeds, UK
| | | | - Malcolm Guiver
- Department Virology, Manchester Royal Infirmary, Manchester, UK
| | - Muir Morton
- Department Renal Medicine, Manchester Royal Infirmary, Manchester, UK
| | - David van Dellen
- Department Renal Transplantation, Manchester Royal Infirmary, Manchester, UK
| | - Eleni Tholouli
- Department Haematology, Manchester Royal Infirmary, Manchester, UK
| | - Robert Wynn
- Paediatric BMT Unit, Royal Manchester Children's Hospital, Manchester, UK
| | - Brendan Clark
- Transplant Immunology, St James's University Hospital, Leeds, UK
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25
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Armstrong LR, Kammerer JS, Haddad MB. Diabetes mellitus among adults with tuberculosis in the USA, 2010-2017. BMJ Open Diabetes Res Care 2020; 8:8/1/e001275. [PMID: 32641300 PMCID: PMC7342266 DOI: 10.1136/bmjdrc-2020-001275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/16/2020] [Accepted: 06/02/2020] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION To describe diabetes trends among adults with incident tuberculosis (TB) disease and examine diabetes-associated TB characteristics and patient outcomes in the USA. RESEARCH DESIGN AND METHODS We examined all 71 855 persons aged ≥20 years with incident TB disease reported to the National Tuberculosis Surveillance System during 2010-2017. We performed multivariable logistic regression, comparing characteristics and outcomes among patients with TB reported to have diabetes and those whose diabetes status was unknown. RESULTS An overall 18% (n=13 281) of the 71 855 adults with incident TB disease were reported as also having diabetes; the annual proportion increased from 15% in 2010 to 22% in 2017. Among patients aged ≥45 years with both TB and diabetes, the adjusted OR for cavitary or sputum smear-positive TB was 1.7 and 1.5, respectively (95% CIs 1.5 to 1.8 and 1.4 to 1.6). Patients with TB and diabetes had 30% greater odds of dying and took longer to achieve negative Mycobacterium tuberculosis cultures and complete treatment. CONCLUSIONS The prevalence of reported diabetes among adults with TB disease has increased. Having diabetes as a comorbidity negatively affects patient outcomes. In accordance with national recommendations, all patients aged ≥45 years and all younger patients who have risk factors for diabetes should be screened for diabetes at the start of TB treatment.
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Affiliation(s)
- Lori R Armstrong
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Steve Kammerer
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maryam B Haddad
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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26
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Ribeiro RM, Graca L. Untangling the immune basis of disease susceptibility. eLife 2020; 9:56886. [PMID: 32406819 PMCID: PMC7224693 DOI: 10.7554/elife.56886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 11/17/2022] Open
Abstract
Interactions between immune cell receptors and proteins that determine disease susceptibility shed light on how different arms of the immune system are involved in three viral infections and Crohn's disease.
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Affiliation(s)
- Ruy M Ribeiro
- Laboratório de Biomatemática, Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Luis Graca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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27
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Debebe BJ, Boelen L, Lee JC, Thio CL, Astemborski J, Kirk G, Khakoo SI, Donfield SM, Goedert JJ, Asquith B. Identifying the immune interactions underlying HLA class I disease associations. eLife 2020; 9:54558. [PMID: 32238263 PMCID: PMC7253178 DOI: 10.7554/elife.54558] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/06/2020] [Indexed: 12/11/2022] Open
Abstract
Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for understanding the etiology of human disease. HLA class I associations are often interpreted in the light of 'protective' or 'detrimental' CD8+ T cell responses which are restricted by the host HLA class I allotype. However, given the diverse receptors which are bound by HLA class I molecules, alternative interpretations are possible. As well as binding T cell receptors on CD8+ T cells, HLA class I molecules are important ligands for inhibitory and activating killer immunoglobulin-like receptors (KIRs) which are found on natural killer cells and some T cells; for the CD94:NKG2 family of receptors also expressed mainly by NK cells and for leukocyte immunoglobulin-like receptors (LILRs) on myeloid cells. The aim of this study is to develop an immunogenetic approach for identifying and quantifying the relative contribution of different receptor-ligand interactions to a given HLA class I disease association and then to use this approach to investigate the immune interactions underlying HLA class I disease associations in three viral infections: Human T cell Leukemia Virus type 1, Human Immunodeficiency Virus type 1 and Hepatitis C Virus as well as in the inflammatory condition Crohn's disease.
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Affiliation(s)
- Bisrat J Debebe
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lies Boelen
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - James C Lee
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
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- Johns Hopkins University, Baltimore, United States.,Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Chloe L Thio
- Johns Hopkins University, Baltimore, United States
| | | | - Gregory Kirk
- Johns Hopkins University, Baltimore, United States
| | - Salim I Khakoo
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, United States
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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28
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Dershem R, Metpally RPR, Jeffreys K, Krishnamurthy S, Smelser DT, Hershfinkel M, Carey DJ, Robishaw JD, Breitwieser GE. Rare-variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations of orphan G protein-coupled receptors. J Biol Chem 2019; 294:18109-18121. [PMID: 31628190 DOI: 10.1074/jbc.ra119.009253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/08/2019] [Indexed: 02/02/2023] Open
Abstract
The pace of deorphanization of G protein-coupled receptors (GPCRs) has slowed, and new approaches are required. Small molecule targeting of orphan GPCRs can potentially be of clinical benefit even if the endogenous receptor ligand has not been identified. Many GPCRs lack common variants that lead to reproducible genome-wide disease associations, and rare-variant approaches have emerged as a viable alternative to identify disease associations for such genes. Therefore, our goal was to prioritize orphan GPCRs by determining their associations with human diseases in a large clinical population. We used sequence kernel association tests to assess the disease associations of 85 orphan or understudied GPCRs in an unselected cohort of 51,289 individuals. Using rare loss-of-function variants, missense variants predicted to be pathogenic or likely pathogenic, and a subset of rare synonymous variants that cause large changes in local codon bias as independent data sets, we found strong, phenome-wide disease associations shared by two or more variant categories for 39% of the GPCRs. To validate the bioinformatics and sequence kernel association test analyses, we functionally characterized rare missense and synonymous variants of GPR39, a family A GPCR, revealing altered expression or Zn2+-mediated signaling for members of both variant classes. These results support the utility of rare variant analyses for identifying disease associations for GPCRs that lack impactful common variants. We highlight the importance of rare synonymous variants in human physiology and argue for their routine inclusion in any comprehensive analysis of genomic variants as potential causes of disease.
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Affiliation(s)
- Ridge Dershem
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Raghu P R Metpally
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Kirk Jeffreys
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Sarathbabu Krishnamurthy
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Diane T Smelser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Michal Hershfinkel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501 Israel
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- Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Janet D Robishaw
- Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Gerda E Breitwieser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822.
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29
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Chang KH, Wu YR, Chen YC, Wu HC, Chen CM. Association between CSF1 and CSF1R Polymorphisms and Parkinson's Disease in Taiwan. J Clin Med 2019; 8:E1529. [PMID: 31554150 DOI: 10.3390/jcm8101529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/26/2022] Open
Abstract
Background: CSF1/CSF1R neuroinflammatory signaling is emerging as an important pathway involved in the pathogenesis of Parkinson’s disease (PD). However, the genetic associations between CSF1/CSF1R and PD have not yet been explored. Methods: We investigated the effects of two functional genetic variants, including CSF1 rs1058885 and CSF1R rs10079250 in a cohort including 502 Taiwanese patients with PD and 511 age- and gender-matched healthy controls. Results: The CSF1 rs1058885 TT genotype was less frequent in PD patients compared with control subjects (odds ratio (OR) = 0.63, 95% confidence interval (CI): 0.43–0.92, p = 0.015). The PD patients also had a lower frequency of the CSF1 rs1058885 T allele compared with the control subjects (OR = 0.80, 95% CI: 0.67–0.96, p = 0.014). No statistically significant differences in allelic and genotypic frequencies of CSF1R rs10079250 between the PD and control subjects were found, even after stratification by age at onset and gender. Conclusion: This study reports a genetic association between CSF1 and PD for the first time.
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30
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Vadva Z, Larsen CE, Propp BE, Trautwein MR, Alford DR, Alper CA. A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies. Cells 2019; 8:E835. [PMID: 31387299 PMCID: PMC6721696 DOI: 10.3390/cells8080835] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, therefore, more useful in genetic correlation with subject phenotype. We describe a new pedigree-based methodology for generating non-ambiguous SNP haplotypes for genetic study. SNP data for haplotype analysis were extracted from a larger Type 1 Diabetes Genetics Consortium SNP dataset based on minor allele frequency variation and redundancy, coverage rate (the frequency of phased haplotypes in which each SNP is defined) and genomic location. Redundant SNPs were eliminated, overall haplotype polymorphism was optimized and the number of undefined haplotypes was minimized. These edited SNP haplotypes from a region containing HLA-DRB1 (DR) and HLA-DQB1 (DQ) both correlated well with HLA-typed DR,DQ haplotypes and differentiated HLA-DR,DQ fragments shared by three pairs of previously identified megabase-length conserved extended haplotypes. In a pedigree-based genetic association assay for type 1 diabetes, edited SNP haplotypes and HLA-typed HLA-DR,DQ haplotypes from the same families generated essentially identical qualitative and quantitative results. Therefore, this edited SNP haplotype method is useful for both genomic polymorphic architecture and genetic association evaluation using SNP markers with diverse minor allele frequencies.
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Affiliation(s)
- Zareen Vadva
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Charles E Larsen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Bennett E Propp
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael R Trautwein
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dennis R Alford
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Chester A Alper
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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31
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Abstract
Parvoviruses are structurally simple viruses with linear single-stranded DNA genomes and nonenveloped icosahedral capsids. They infect a wide range of animals from insects to humans. Parvovirus B19 is a long-known human pathogen, whereas adeno-associated viruses are nonpathogenic. Since 2005, many parvoviruses have been discovered in human-derived samples: bocaviruses 1-4, parvovirus 4, bufavirus, tusavirus, and cutavirus. Some human parvoviruses have already been shown to cause disease during acute infection, some are associated with chronic diseases, and others still remain to be proven clinically relevant-or harmless commensals, a distinction not as apparent as it might seem. One initially human-labeled parvovirus might not even be a human virus, whereas another was originally overlooked due to inadequate diagnostics. The intention of this review is to follow the rocky road of emerging human parvoviruses from discovery of a DNA sequence to current and future clinical status, highlighting the perils along the way.
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Geraghty DE, Thorball CW, Fellay J, Thomas R. Effect of Fc Receptor Genetic Diversity on HIV-1 Disease Pathogenesis. Front Immunol 2019; 10:970. [PMID: 31143176 PMCID: PMC6520634 DOI: 10.3389/fimmu.2019.00970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 04/15/2019] [Indexed: 11/21/2022] Open
Abstract
Fc receptor (FcR) genes collectively have copy number and allelic polymorphisms that have been implicated in multiple inflammatory and autoimmune diseases. This variation might also be involved in etiology of infectious diseases. The protective role of Fc-mediated antibody-function in HIV-1 immunity has led to the investigation of specific polymorphisms in FcR genes on acquisition, disease progression, and vaccine efficacy in natural history cohorts. The purpose of this review is not only to explore these known HIV-1 host genetic associations, but also to re-evaluate them in the context of genome-wide data. In the current era of effective anti-retroviral therapy, the potential impact of such variation on post-treatment cohorts cannot go unheeded and is discussed here in the light of current findings. Specific polymorphisms associating with HIV-1 pathogenesis have previously been genotyped by assays that captured only the single-nucleotide polymorphism (SNP) of interest without relative information of neighboring variants. With recent technological advances, variation within these genes can now be characterized using next-generation sequencing, allowing precise annotation of the whole chromosomal region. We herein also discuss updates in the annotation of common FcR variants that have been previously associated with HIV-1 pathogenesis.
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Affiliation(s)
- Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rasmi Thomas
- U. S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
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Abstract
The Natural Cytotoxicity Receptors (NCRs), NKp46, NKp44, and NKp30, were some of the first human activating Natural Killer (NK) cell receptors involved in the non-MHC-restricted recognition of tumor cells to be cloned over 20 years ago. Since this time many host- and pathogen-encoded ligands have been proposed to bind the NCRs and regulate the cytotoxic and cytokine-secreting functions of tissue NK cells. This diverse set of NCR ligands can manifest on the surface of tumor or virus-infected cells or can be secreted extracellularly, suggesting a remarkable NCR polyfunctionality that regulates the activity of NK cells in different tissue compartments during steady state or inflammation. Moreover, the NCRs can also be expressed by other innate and adaptive immune cell subsets under certain tissue conditions potentially conferring NK recognition programs to these cells. Here we review NCR biology in health and disease with particular reference to how this important class of receptors regulates the functions of tissue NK cells as well as confer NK cell recognition patterns to other innate and adaptive lymphocyte subsets. Finally, we highlight how NCR biology is being harnessed for novel therapeutic interventions particularly for enhanced tumor surveillance.
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Affiliation(s)
- Alexander David Barrow
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Claudia Jane Martin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
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Kishore A, Petrek M. Next-Generation Sequencing Based HLA Typing: Deciphering Immunogenetic Aspects of Sarcoidosis. Front Genet 2018; 9:503. [PMID: 30410504 PMCID: PMC6210504 DOI: 10.3389/fgene.2018.00503] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/05/2018] [Indexed: 12/31/2022] Open
Abstract
Unraveling of the HLA-related immunogenetic basis of several immune disorders is complex due to the extensive HLA polymorphism and strong linkage-disequilibrium between HLA loci. A lack of in phase sequence information, a relative deficiency of high resolution genotyping including non-coding regions and ambiguous haplotype assignment make it difficult to compare findings across association studies and to attribute a causal role to specific HLA alleles/haplotypes in disease susceptibility and modification of disease phenotypes. Earlier, historical antibody and DNA-based methods of HLA typing, primarily of low resolution at antigen/alellic group levels, yielded "indicative" findings which were partially improved by high-resolution DNA-based typing. Only recently, next-generation sequencing (NGS) approaches based on deep-sequencing of the complete HLA genes combined with bioinformatics tools began to provide the access to complete information at an allelic level. Analyzing HLA with NGS approaches, therefore, promises to provide further insight in the etiopathogenesis of several immune disorders in which HLA associations have been implicated. These range from coeliac disease and rheumatological conditions to even more complex disorders, such as type-1 diabetes, systemic lupus erythematosus and sarcoidosis. A systemic disease of unknown etiology, sarcoidosis has previously been associated with numerous HLA variants and also other gene polymorphisms, often in linkage with the HLA region. To date, the biological significance of these associations has only partially been defined. Therefore, more precise assignments of HLA alleles/haplotypes using NGS approaches could help to elucidate the exact role of HLA variation in the multifaceted etiopathogenesis of sarcoidosis, including epigenetic mechanisms. NGS-based HLA analyses may be also relevant for defining variable clinical phenotypes and for predicting the disease course or the response to current/plausible novel therapies.
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Affiliation(s)
- Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czechia
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35
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Amstutz U, Schaerer D, Andrey G, Wirthmueller U, Largiadèr CR. An SSP-PCR method for the rapid detection of disease-associated alleles HLA-A*29 and HLA-B*51. HLA 2018; 92:90-93. [PMID: 29766667 DOI: 10.1111/tan.13296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 05/07/2018] [Indexed: 11/28/2022]
Abstract
HLA-A*29 and HLA-B*51 are associated with birdshot uveitis and Behçet's disease, respectively, and are used as a diagnostic criterion in patients with suspected disease, requiring their detection in diagnostic laboratories. While commercial tests for individual HLA alleles are available for other disease-associated HLA variants, no similar allele-specific assays are available for HLA-A*29 and HLA-B*51. Here, we report sequence-specific priming-polymerase chain reaction (SSP-PCR) methods for the detection of HLA-A*29 and HLA-B*51 using a single PCR reaction per allele. The assays were tested in 30 and 32 previously HLA-typed samples, respectively, representing >97% of HLA-A alleles and >93% of HLA-B alleles in a European population. A concordance of 100% was observed with previous typing results, validating these methods for use in a diagnostic or research context.
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Affiliation(s)
- U Amstutz
- University Institute of Clinical Chemistry, Center for Laboratory Medicine, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
| | - D Schaerer
- University Institute of Clinical Chemistry, Center for Laboratory Medicine, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
| | - G Andrey
- University Institute of Clinical Chemistry, Center for Laboratory Medicine, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
| | - U Wirthmueller
- University Institute of Clinical Chemistry, Center for Laboratory Medicine, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
| | - C R Largiadèr
- University Institute of Clinical Chemistry, Center for Laboratory Medicine, Inselspital Bern University Hospital, University of Bern, Bern, Switzerland
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36
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McLuckie AJ, Barrs VR, Lindsay S, Aghazadeh M, Sangster C, Beatty JA. Molecular Diagnosis of Felis catus Gammaherpesvirus 1 (FcaGHV1) Infection in Cats of Known Retrovirus Status with and without Lymphoma. Viruses 2018; 10:E128. [PMID: 29538321 DOI: 10.3390/v10030128] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The pathogenicity of Felis catus gammaherpesvirus 1 (FcaGHV1), a common infection of domestic cats, is unknown. To explore an association between FcaGHV1 detection and feline lymphoma, a retrospective, cross-sectional, disease-association study was conducted. The infection status of all cats for feline immunodeficiency virus and feline leukaemia virus was determined. Neither a molecular diagnosis of FcaGHV1 nor whole-blood FcaGHV1 load was related to outcome in 122 lymphoma cases compared with 71 controls matched for age and sex. Molecular analysis of lymphoma-derived DNA paired with autologous uninvolved tissue did not suggest restriction of FcaGHV1 DNA to tumour tissue. FcaGHV1 DNA detection was associated with significantly shorter survival in lymphoma cases, an observation that could not be adequately explained by treatment differences. In addition, regressive feline leukaemia virus infection was identified as a risk factor for lymphoma. A history of fighting or roaming was identified as a novel epidemiological risk factor for FcaGHV1 detection, lending support to intercat aggression as a potential route of transmission. Studies investigating the cellular location and expression of FcaGHV1 are indicated to assist in ruling out a lymphomagenic role for this virus. Prospective investigation of FcaGHV1 DNA detection as a prognostic marker in feline lymphoma is warranted.
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Gębura K, Świerkot J, Wysoczańska B, Korman L, Nowak B, Wiland P, Bogunia-Kubik K. Polymorphisms within Genes Involved in Regulation of the NF-κB Pathway in Patients with Rheumatoid Arthritis. Int J Mol Sci 2017; 18:E1432. [PMID: 28677621 DOI: 10.3390/ijms18071432] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 02/06/2023] Open
Abstract
Genes involved in regulation of the nuclear factor-κB (NF-κB)-pathway are suggested to play a role in pathogenesis of rheumatoid arthritis (RA). In the present study, genetic polymorphisms of TLR2, TLR4, TLR9 and NF-κB1 genes were investigated to assess their associations with RA susceptibility, progression and response to anti-TNF-α therapy. A group of 110 RA patients and 126 healthy individuals were genotyped for TLR2 (rs111200466), TLR4 (rs4986790, rs4986791), TLR9 (rs5743836, rs187084) and NF-κB1 (rs28362491) alleles. The presence of the TLR9 -1486 T variant (p < 0.0001) and its homozygosity (p < 0.0001) were found to be associated with disease susceptibility. The TLR9 -1237 C allele was associated with predisposition to RA in females only (p = 0.005). Moreover, the TLR4 rs4986791 G (rs4986790 T) alleles were more frequently detected among patients with the stage IV disease (p = 0.045), and were associated with more effective response to anti-TNF-α therapy (p = 0.012). More efficient response to anti-TNF-α treatment was also observed in patients with del within the NF-κB1 gene (p = 0.047), while for the TLR9 -1486 T homozygotes, the treatment was ineffective (p = 0.018). TLR polymorphisms affect disease susceptibility and response to therapy with TNF-α inhibitors in RA patients of Caucasian origin.
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38
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Overton NL, Simpson A, Bowyer P, Denning DW. Genetic susceptibility to severe asthma with fungal sensitization. Int J Immunogenet 2017; 44:93-106. [PMID: 28371335 DOI: 10.1111/iji.12312] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/04/2017] [Accepted: 02/23/2017] [Indexed: 12/30/2022]
Abstract
Severe asthma is problematic and its pathogenesis poorly understood. Fungal sensitization is common, and many patients with severe asthma with fungal sensitization (SAFS), used to denote this subgroup of asthma, respond to antifungal therapy. We have investigated 325 haplotype-tagging SNPs in 22 candidate genes previously associated with aspergillosis in patients with SAFS, with comparisons in atopic asthmatics and healthy control patients, of whom 47 SAFS, 279 healthy and 152 atopic asthmatic subjects were genotyped successfully. Significant associations with SAFS compared with atopic asthma included Toll-like receptor 3 (TLR3) (p = .009), TLR9 (p = .025), C-type lectin domain family seven member A (dectin-1) (p = .043), interleukin-10 (IL-10) (p = .0010), mannose-binding lectin (MBL2) (p = .007), CC-chemokine ligand 2 (CCL2) (2 SNPs, p = .025 and .041), CCL17 (p = .002), plasminogen (p = .049) and adenosine A2a receptor (p = .024). These associations differ from those found in ABPA in asthma, indicative of contrasting disease processes. Additional and broader genetic association studies in SAFS, combined with experimental work, are likely to contribute to our understanding of different phenotypes of problematic asthma.
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Affiliation(s)
- N L Overton
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, The University of Manchester, Manchester, UK.,Manchester Fungal Infection Group (MFIG), The University of Manchester, Manchester, UK
| | - A Simpson
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, The University of Manchester, Manchester, UK
| | - P Bowyer
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, The University of Manchester, Manchester, UK.,Manchester Fungal Infection Group (MFIG), The University of Manchester, Manchester, UK
| | - D W Denning
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, The University of Manchester, Manchester, UK.,Manchester Fungal Infection Group (MFIG), The University of Manchester, Manchester, UK
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39
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Maadooliat M, Bansal NK, Upadhya J, Farazi MR, Li X, He MM, Hebbring SJ, Ye Z, Schrodi SJ. The Decay of Disease Association with Declining Linkage Disequilibrium: A Fine Mapping Theorem. Front Genet 2016; 7:217. [PMID: 28018425 PMCID: PMC5149547 DOI: 10.3389/fgene.2016.00217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/28/2016] [Indexed: 11/13/2022] Open
Abstract
Several important and fundamental aspects of disease genetics models have yet to be described. One such property is the relationship of disease association statistics at a marker site closely linked to a disease causing site. A complete description of this two-locus system is of particular importance to experimental efforts to fine map association signals for complex diseases. Here, we present a simple relationship between disease association statistics and the decline of linkage disequilibrium from a causal site. Specifically, the ratio of Chi-square disease association statistics at a marker site and causal site is equivalent to the standard measure of pairwise linkage disequilibrium, r2. A complete derivation of this relationship from a general disease model is shown. Quite interestingly, this relationship holds across all modes of inheritance. Extensive Monte Carlo simulations using a disease genetics model applied to chromosomes subjected to a standard model of recombination are employed to better understand the variation around this fine mapping theorem due to sampling effects. We also use this relationship to provide a framework for estimating properties of a non-interrogated causal site using data at closely linked markers. Lastly, we apply this way of examining association data from high-density genotyping in a large, publicly-available data set investigating extreme BMI. We anticipate that understanding the patterns of disease association decay with declining linkage disequilibrium from a causal site will enable more powerful fine mapping methods and provide new avenues for identifying causal sites/genes from fine-mapping studies.
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Affiliation(s)
- Mehdi Maadooliat
- Department of Mathematics, Statistics and Computer Science, Marquette UniversityMilwaukee, WI, USA; Center for Human Genetics, Marshfield Clinic Research FoundationMarshfield, WI, USA
| | - Naveen K Bansal
- Department of Mathematics, Statistics and Computer Science, Marquette University Milwaukee, WI, USA
| | - Jiblal Upadhya
- Department of Mathematics, Statistics and Computer Science, Marquette University Milwaukee, WI, USA
| | - Manzur R Farazi
- Department of Mathematics, Statistics and Computer Science, Marquette University Milwaukee, WI, USA
| | - Xiang Li
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation Marshfield, WI, USA
| | - Max M He
- Center for Human Genetics, Marshfield Clinic Research FoundationMarshfield, WI, USA; Biomedical Informatics Research Center, Marshfield Clinic Research FoundationMarshfield, WI, USA; Computation and Informatics in Biology and Medicine, University of Wisconsin-MadisonMadison, WI, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research FoundationMarshfield, WI, USA; Computation and Informatics in Biology and Medicine, University of Wisconsin-MadisonMadison, WI, USA
| | - Zhan Ye
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation Marshfield, WI, USA
| | - Steven J Schrodi
- Center for Human Genetics, Marshfield Clinic Research FoundationMarshfield, WI, USA; Computation and Informatics in Biology and Medicine, University of Wisconsin-MadisonMadison, WI, USA
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40
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Weiskopf D, Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, De Silva AD, Phillips E, Mallal S, Premawansa S, Premawansa G, Wijewickrama A, Peters B, Sette A. HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4+ T-Cell Responses. J Infect Dis 2016; 214:1117-24. [PMID: 27443615 DOI: 10.1093/infdis/jiw309] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/15/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Each year dengue virus (DENV) infects 400 million human but causes symptomatic disease in only a subset of patients, suggesting that host genetic factors may play a role. HLA molecules that restrict T-cell responses are one of the most polymorphic host factors in humans. METHODS Here we map HLA DRB1-restricted DENV-specific epitopes in individuals previously exposed to DENV, to identify the breadth and specificity of CD4(+) T-cell responses. To investigate whether HLA-specific variations in the magnitude of response might predict associations between dengue outcomes and HLA-DRB1 alleles, we assembled samples from hospitalized patients with known severity of disease. RESULTS The capsid protein followed by nonstructural protein 3 (NS3), NS2A, and NS5 were the most targeted proteins. We further noticed a wide variation in magnitude of T-cell responses as a function of the restricting DRB1 allele and found several HLA alleles that showed trends toward a lower risk of hospitalized disease were associated with a higher magnitude of T-cell responses. CONCLUSIONS Comprehensive identification of unique CD4(+) T-cell epitopes across the 4 DENV serotypes allows the testing of T-cell responses by use of a simple, approachable technique and points to important implications for vaccine design.
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Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Michael A Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Patrick H O'Rourke
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Aruna D De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California Genetech Research Institute
| | - Elizabeth Phillips
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Sunil Premawansa
- Department of Zoology and Environmental Science, Science Faculty, University of Colombo
| | | | | | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
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41
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Abstract
In order to provide specificity for T cell responses against pathogens and tumours, major histocompatibility complex (MHC) class I molecules present high-affinity peptides at the cell surface to T cells. A key player for peptide loading is the MHC class I-dedicated chaperone tapasin. Recently we discovered a second MHC class I-dedicated chaperone, the tapasin-related protein TAPBPR. Here, we review the major steps in the MHC class I pathway and the TAPBPR data. We discuss the potential function of TAPBPR in the MHC class I pathway and the involvement of this previously uncharacterised protein in human health and disease.
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Affiliation(s)
- C Hermann
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
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42
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Suravajhala P, Kogelman LJA, Mazzoni G, Kadarmideen HN. Potential role of lncRNA cyp2c91-protein interactions on diseases of the immune system. Front Genet 2015; 6:255. [PMID: 26284111 PMCID: PMC4516971 DOI: 10.3389/fgene.2015.00255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/15/2015] [Indexed: 01/09/2023] Open
Abstract
With unprecedented increase in next generation sequencing technologies, there has been a persistent interest on transcript profiles of long non-coding RNAs (lncRNAs) and protein-coding genes forming an interaction network. Apart from protein–protein interaction (PPI), gene network models such as Weighted Gene Co-expression Network Analysis (WGCNA) are used to functionally annotate lncRNAs in identifying their potential disease associations. To address this, studies have led to characterizing transcript structures and understanding expression profiles mediating regulatory roles. In the current exploratory analysis, we show how a lncRNA – cyp2c91 contributes to the transcriptional regulation localized to cytoplasm thereby making refractory environment for transcription. By applying network methods and pathway analyses on genes related to a disease such as obesity and systemic lupus erythematosus, we show that we can gain deeper insight in biological processes such as the perturbances in immune system, and get a better understanding of the systems biology of diseases.
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Affiliation(s)
- Prashanth Suravajhala
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg Denmark
| | - Lisette J A Kogelman
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg Denmark
| | - Gianluca Mazzoni
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg Denmark
| | - Haja N Kadarmideen
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg Denmark
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43
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Zhang C, Liu S, Hou S, Lei B, Zheng X, Xiao X, Kijlstra A, Yang P. MIF gene polymorphisms confer susceptibility to Vogt-Koyanagi-Harada syndrome in a Han Chinese population. Invest Ophthalmol Vis Sci 2013; 54:7734-8. [PMID: 24194192 DOI: 10.1167/iovs.13-12187] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE The aim of the study was to determine the association of macrophage migration inhibitory factor (MIF) gene polymorphisms with Vogt-Koyanagi-Harada (VKH) syndrome. METHODS A total of 600 Han Chinese VKH patients and 600 healthy controls were genotyped for rs755622 and rs2096525 of MIF by PCR-restriction fragment length polymorphism (PCR-RFLP) assay. Data were analyzed by χ(2) analysis. RESULTS Genotype distribution in controls was in Hardy-Weinberg equilibrium. The frequencies of the rs755622 GG genotype and G allele were significantly lower in VKH patients compared with controls (Pc = 0.006 and 0.016). Stratification analysis showed decreased frequencies of the rs755622 GG genotype and G allele in patients, respectively with headache, tinnitus, alopecia, poliosis or vitiligo compared with controls (all Pc < 0.05). rs2096525 genotype and allele frequencies were not different between VKH patients and controls. However, a lower frequency of the rs2096525 TT genotype was observed in patients with headache compared with controls (Pc < 0.05). The frequencies of the rs2096525 T allele in patients with headache or vitiligo were significantly decreased compared with controls (Pc = 8.54 × 10(-4) and 0.012). In addition, the results showed a significantly increased frequency of the combined rs755622/rs2096525 CT haplotype and a decreased frequency of the GT haplotype in VKH patients compared with controls. CONCLUSIONS Our study identified a strong association of rs755622 with VKH syndrome and certain clinical features. rs2096525 was associated with certain clinical features of VKH syndrome. The results also suggested that the CT and GT haplotypes were associated with VKH syndrome.
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Affiliation(s)
- Chunxia Zhang
- Jinan Mingshui Eye Hospital, Jinan, People's Republic of China
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44
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Abstract
High throughput technologies have been applied to investigate the underlying mechanisms of complex diseases, identify disease-associations and help to improve treatment. However it is challenging to derive biological insight from conventional single gene based analysis of "omics" data from high throughput experiments due to sample and patient heterogeneity. To address these challenges, many novel pathway and network based approaches were developed to integrate various "omics" data, such as gene expression, copy number alteration, Genome Wide Association Studies, and interaction data. This review will cover recent methodological developments in pathway analysis for the detection of dysregulated interactions and disease-associated subnetworks, prioritization of candidate disease genes, and disease classifications. For each application, we will also discuss the associated challenges and potential future directions.
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45
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Halldórsson BV, Sharan R. Network-based interpretation of genomic variation data. J Mol Biol 2013; 425:3964-9. [PMID: 23886866 DOI: 10.1016/j.jmb.2013.07.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/02/2013] [Accepted: 07/16/2013] [Indexed: 02/02/2023]
Abstract
Advances in sequencing technologies are allowing genome-wide association studies at an ever-growing scale. The interpretation of these studies requires dealing with statistical and combinatorial challenges, owing to the multi-factorial nature of human diseases and the huge space of genomic markers that are being monitored. Recently, it was proposed that using protein-protein interaction network information could help in tackling these challenges by restricting attention to markers or combinations of markers that map to close proteins in the network. In this review, we survey techniques for integrating genomic variation data with network information to improve our understanding of complex diseases and reveal meaningful associations.
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Affiliation(s)
- Bjarni V Halldórsson
- School of Science and Engineering, Reykjavík University, 101 Reykjavík, Iceland.
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46
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Abstract
Interactions between killer immunoglobulin-like receptors (KIRs) and their HLA-A, -B, and -C ligands diversify the functions of human natural killer cells. Consequently, combinations of KIR and HLA genotypes affect resistance to infection and autoimmunity, success of reproduction and outcome of hematopoietic cell transplantation. HLA-C, with its C1 and C2 epitopes, evolved in hominids to be specialized KIR ligands. The system’s foundation was the C1 epitope, with C2 a later addition, by several million years. The human inhibitory receptor for C1 is encoded by KIR2DL2/3, a gene having two divergent allelic lineages: KIR2DL2 is a B KIR haplotype component and KIR2DL3 an A KIR haplotype component. Although KIR2DL2 and KIR2DL3 exhibit quantitative differences in specificity and avidity for HLA-C, they qualitatively differ in their genetics, functional effect, and clinical influence. This is due to linkage disequilibrium between KIR2DL2 and KIR2DS2, a closely related activating receptor that was selected for lost recognition of HLA-C.
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Affiliation(s)
- Achim K Moesta
- Genome Analysis Unit, Discovery Research, Amgen Inc., South San Francisco , CA, USA
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Abstract
Viral metagenomics has recently yielded numerous previously uncharacterized viral genomes from human and animal samples. We review some of the metagenomics tools and strategies to determine which orphan viruses are likely pathogens. Disease association studies compare viral prevalence in patients with unexplained symptoms versus healthy individuals but require these case and control groups to be closely matched epidemiologically. The development of an antibody response in convalescent serum can temporarily link symptoms with a recent infection. Neutralizing antibody detection require often difficult cell culture virus amplification. Antibody binding assays require proper antigen synthesis and positive control sera to set assay thresholds. High levels of viral genetic diversity within orphan viral groups, frequent co-infections, low or rare pathogenicity, and chronic virus shedding, can all complicate disease association studies. The limited availability of matched cases and controls sample sets from different age groups and geographic origins is a major block for estimating the pathogenic potential of recently characterized orphan viruses. Current limitations on the practical use of deep sequencing for viral diagnostics are listed.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA
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Abstract
The newly established family Anelloviridae includes a number of viruses infecting humans (Torque teno viruses) and other animal species. The ones infecting domestic swine and wild boar are nowadays named Torque teno sus viruses (TTSuV), which are small circular single-stranded DNA viruses highly prevalent in the pig population. So far, two genetically distinct TTSuV species are infecting swine. Both TTSuVs appear to efficiently spread by vertical and horizontal transmission routes; in fact, foetuses may be infected and the prevalence and viral loads increase by age of the animals. Detailed immunological studies on TTSuVs are still lacking, but it seems that there are no efficient immunological responses limiting viraemia. These viruses are currently receiving more attention due to the latest results on disease association. Torque teno sus viruses have been circulating unnoticed in pigs for a long time, and even considered non-pathogenic by themselves; there is increasing evidence that points to influence the development of some diseases or even affect their outcome. Such link has been mainly established with porcine circovirus diseases.
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Affiliation(s)
- T Kekarainen
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain.
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Han W, Li X, Fu X. The macro domain protein family: structure, functions, and their potential therapeutic implications. Mutat Res 2011; 727:86-103. [PMID: 21421074 PMCID: PMC7110529 DOI: 10.1016/j.mrrev.2011.03.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 05/02/2023]
Abstract
Macro domains are ancient, highly evolutionarily conserved domains that are widely distributed throughout all kingdoms of life. The 'macro fold' is roughly 25kDa in size and is composed of a mixed α-β fold with similarity to the P loop-containing nucleotide triphosphate hydrolases. They function as binding modules for metabolites of NAD(+), including poly(ADP-ribose) (PAR), which is synthesized by PAR polymerases (PARPs). Although there is a high degree of sequence similarity within this family, particularly for residues that might be involved in catalysis or substrates binding, it is likely that the sequence variation that does exist among macro domains is responsible for the specificity of function of individual proteins. Recent findings have indicated that macro domain proteins are functionally promiscuous and are implicated in the regulation of diverse biological functions, such as DNA repair, chromatin remodeling and transcriptional regulation. Significant advances in the field of macro domain have occurred in the past few years, including biological insights and the discovery of novel signaling pathways. To provide a framework for understanding these recent findings, this review will provide a comprehensive overview of the known and proposed biochemical, cellular and physiological roles of the macro domain family. Recent data that indicate a critical role of macro domain regulation for the proper progression of cellular differentiation programs will be discussed. In addition, the effect of dysregulated expression of macro domain proteins will be considered in the processes of tumorigenesis and bacterial pathogenesis. Finally, a series of observations will be highlighted that should be addressed in future efforts to develop macro domains as effective therapeutic targets.
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Key Words
- adpr, adp-ribose
- aplf, aprataxin pnk-like factor
- bares, bacterial-produce adp-ribosylating exotoxins
- marts, mono-adp-ribosyltransferases
- ar, androgen receptor
- ber, base excision repair
- bcl2, b cell lymphoma 2
- coast6, collaborator of stat6
- chfr, checkpoint protein with fha and ring domain
- cbp, creb-binding protein
- chip, chromatin immunoprecipitation
- dsbs, dna double-stranded breaks
- 3d, three-dimensional
- dt, diphtheria toxin
- erα, estrogen receptor α
- eta, exotoxin a
- emt, epithelial–mesenchymal transition
- itc, isothermal titration calorimetry
- iaps, inhibitors of apoptosis
- ks, kabuki syndrome
- msci, meiotic sex chromosome inactivation
- nf-κb, nuclear factor-kappab
- oaadpr, o-acetyl-adp-ribose
- par, poly(adp-ribose)
- parps, par polymerases
- parg, par glycohydrolase
- parylation, poly(adp-ribosyl)ation
- parbms, par binding motifs
- ptms, posttranslational modifications
- pbz, par binding zinc finger
- rnap ii, rna polymerase ii
- stat6, signal transducer and activator of transcription-6
- sfv, semliki forest virus
- ssbr, single-strand break repair
- sts, staurosporine
- tnf, tumor necrosis factor
- trf1, telomeric repeat binding factor-1
- macro domain family
- structural feature
- posttranslational modifications
- biological function
- disease association
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Affiliation(s)
- Weidong Han
- Corresponding author. Tel.: +86 10 6693 7463; fax: +86 10 6693 7516.
| | | | - Xiaobing Fu
- Corresponding author. Tel.: +86 10 6898 9955; fax: +86 10 6898 9955.
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Venter M, Visser A, Lassauniere R. Human polyomaviruses, WU and KI in HIV exposed children with acute lower respiratory tract infections in hospitals in South Africa. J Clin Virol 2009; 44:230-4. [PMID: 19171499 PMCID: PMC7172267 DOI: 10.1016/j.jcv.2008.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 12/03/2008] [Accepted: 12/11/2008] [Indexed: 11/27/2022]
Abstract
BACKGROUND The importance of two recently identified polyomaviruses, WUV and KIV, as respiratory pathogens in populations with a high HIV prevalence needs to be defined, since human polyomaviruses can cause significant morbidity and mortality in patients with immunosuppression. Geographic distribution and disease association of WUV and KIV genotypes are not yet clearly defined. OBJECTIVES To investigate the prevalence of WUV and KIV in HIV-positive and HIV-negative patients with respiratory infections in hospitals in South Africa and determine their genotypes. STUDY DESIGN Specimens from patients with acute respiratory infections from hospitals serving Pretoria were screened for WUV and KIV. Positive specimens were sequenced and subjected to phylogenetic analysis. RESULTS WUV was identified in (7%) and KIV in (1%) of mainly pediatric patients. Co-infections were common in WUV- and KIV-infected patients (71% and 66.6%, respectively); 57% of patients with WUV and 33% of patients with KIV were HIV-positive while the HIV prevalence in the respiratory virus patient group screened in this study was 33% WUV and KIV patients presented with moderate to severe lower respiratory tract disease. Four distinct and 2 unique WUV strains were identified clustering into 2 of 4 globally identified genotypes. KIV strains were identical to strains from Sweden. CONCLUSION WUV is frequently detected in HIV-infected patients with respiratory disease, but its role as respiratory pathogen remains uncertain.
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Affiliation(s)
- Marietjie Venter
- Department of Medical Virology, University of Pretoria, South Africa.
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