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Yang Q, Berkman AM, Ezekian JE, Rosamilia M, Rosenfeld JA, Liu P, Landstrom AP. Determining the Likelihood of Disease Pathogenicity Among Incidentally Identified Genetic Variants in Rare Dilated Cardiomyopathy-Associated Genes. J Am Heart Assoc 2022; 11:e025257. [PMID: 36129056 DOI: 10.1161/jaha.122.025257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background As utilization of clinical exome sequencing (ES) has expanded, criteria for evaluating the diagnostic weight of incidentally identified variants are critical to guide clinicians and researchers. This is particularly important in genes associated with dilated cardiomyopathy (DCM), which can cause heart failure and sudden death. We sought to compare the frequency and distribution of incidentally identified variants in DCM-associated genes between a clinical referral cohort with those in control and known case cohorts to determine the likelihood of pathogenicity among those undergoing genetic testing for non-DCM indications. Methods and Results A total of 39 rare, non-TTN DCM-associated genes were identified and evaluated from a clinical ES testing referral cohort (n=14 005, Baylor Genetic Laboratories) and compared with a DCM case cohort (n=9442) as well as a control cohort of population variants (n=141 456) derived from the gnomAD database. Variant frequencies in each cohort were compared. Signal-to-noise ratios were calculated comparing the DCM and ES cohort with the gnomAD cohort. The likely pathogenic/pathogenic variant yield in the DCM cohort (8.2%) was significantly higher than in the ES cohort (1.9%). Based on signal-to-noise and correlation analysis, incidental variants found in FLNC, RBM20, MYH6, DSP, ABCC9, JPH2, and NEXN had the greatest chance of being DCM-associated. Conclusions The distribution of pathogenic variants between the ES cohort and the DCM case cohort was gene specific, and variants found in the ES cohort were similar to variants found in the control cohort. Incidentally identified variants in specific genes are more associated with DCM than others.
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Affiliation(s)
- Qixin Yang
- Department of Pediatrics, Division of Cardiology Duke University School of Medicine Durham NC.,Department of Cardiology The First Affiliated Hospital, College of Medicine, Zhejiang University Hangzhou China
| | - Amy M Berkman
- Department of Pediatrics, Division of Cardiology Duke University School of Medicine Durham NC
| | - Jordan E Ezekian
- Department of Pediatrics, Division of Cardiology Duke University School of Medicine Durham NC
| | - Michael Rosamilia
- Department of Pediatrics, Division of Cardiology Duke University School of Medicine Durham NC
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics Baylor College of Medicine and Baylor Genetics Laboratories Houston TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics Baylor College of Medicine and Baylor Genetics Laboratories Houston TX
| | - Andrew P Landstrom
- Department of Pediatrics, Division of Cardiology Duke University School of Medicine Durham NC.,Department of Cell Biology Duke University School of Medicine Durham NC
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Ghanbarnezhad MM, Shahsavani MB, Mali PS, Upadhyay M, Kumar A, Albaghlani RM, Niazi A, Yousefi R. Developing a novel exenatide-based incretin mimic (αB-Ex): Expression, purification and structural-functional characterization. Biochim Biophys Acta Gen Subj 2022; 1866:130150. [DOI: 10.1016/j.bbagen.2022.130150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 10/18/2022]
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3
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A novel method for the chaperone aided and efficient production of human proinsulin in the prokaryotic system. J Biotechnol 2022; 346:35-46. [DOI: 10.1016/j.jbiotec.2022.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023]
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4
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Gomes F, Watanabe L, Vianez J, Nunes M, Cardoso J, Lima C, Schneider H, Sampaio I. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PLoS One 2019; 14:e0212755. [PMID: 30802266 PMCID: PMC6388931 DOI: 10.1371/journal.pone.0212755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. Results The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. Conclusion In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management.
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Affiliation(s)
- Fátima Gomes
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
- * E-mail:
| | - Luciana Watanabe
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
| | - João Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Márcio Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Jedson Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
- Postgraduate Program in Virology (PPGV), Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Clayton Lima
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Horacio Schneider
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
| | - Iracilda Sampaio
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
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Alpha B-crystallin C-802G polymorphism and colorectal cancer susceptibility and clinical outcome in Chinese population. Sci Rep 2018; 8:11731. [PMID: 30082880 PMCID: PMC6078991 DOI: 10.1038/s41598-018-29589-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/16/2018] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide and Alpha B-crystallin (CRYAB) protein has been identified as a prognostic biomarker for CRC. We evaluated CRYAB C-802G (rs14133)polymorphism in association with CRC risk and survival in Chinese population. We genotyped for CRYAB C-802G (rs14133), A-1215G (rs2228387) and intron 2 (rs2070894), and assessed their associations with CRC in a case-control study of 441 CRC cases and 500 healthy controls. We also analyzed this polymorphism in relation to overall survival in CRC patients. A significantly different frequency distribution was found in CRYAB C-802G genotypes, but not in A-1215G and intron2 genotypes, between the cases and the controls. Under multivariable logistic regression adjusted for age and gender, CG/GG genotype carriers were associated with increased risk of CRC (OR 1.754, 95% CI 1.338–2.301, P < 0.001) when compared with CC genotype carriers. Multivariate Cox proportional hazards model showed that patients with CG/GG genotype had significant shorter survival time than those with CC genotype, after adjustment for gender and TNM stage (HR 2.347, 95% CI 1.719–3.204, P < 0.001), and after adjustment for gender and tumor grade (HR 2.871, 95% CI 2.121–3.887, P < 0.001), respectively. Our results demonstrated that CG/GG at CRYAB C-802G is correlated with CRC susceptibility and this polymorphism may be an useful marker for clinical outcome of CRC.
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Abstract
αB-crystallin is a widely expressed member of the small heat shock protein family that protects cells from stress by its dual function as a molecular chaperone to preserve proteostasis and as a cell death antagonist that negatively regulates components of the conserved apoptotic cell death machinery. Deregulated expression of αB-crystallin occurs in a broad array of solid tumors and has been linked to tumor progression and poor clinical outcomes. This review will focus on new insights into the molecular mechanisms by which oncogenes, oxidative stress, matrix detachment and other tumor microenvironmental stressors deregulate αB-crystallin expression. We will also review accumulating evidence pointing to an essential role for αB-crystallin in the multi-step metastatic cascade whereby tumor cells colonize distant organs by circumventing a multitude of barriers to cell migration and survival. Finally, we will evaluate emerging strategies to therapeutically target αB-crystallin and/or interacting proteins to selectively activate apoptosis and/or derail the metastatic cascade in an effort to improve outcomes for patients with metastatic disease.
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CRYAB-650 C>G (rs2234702) affects susceptibility to Type 1 diabetes and IAA-positivity in Swedish population. Hum Immunol 2012; 73:759-66. [DOI: 10.1016/j.humimm.2012.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 04/06/2012] [Accepted: 04/16/2012] [Indexed: 10/28/2022]
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Fontanesi L, Davoli R, Milc J, Russo V. Linkage mapping of the alpha-B-crystallin (CRYAB) gene to porcine chromosome 9. Anim Genet 2000; 31:287-8. [PMID: 11086547 DOI: 10.1046/j.1365-2052.2000.00646.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- L Fontanesi
- DIPROVAL-Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Reggio Emilia, Italy.
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Vicart P, Caron A, Guicheney P, Li Z, Prévost MC, Faure A, Chateau D, Chapon F, Tomé F, Dupret JM, Paulin D, Fardeau M. A missense mutation in the alphaB-crystallin chaperone gene causes a desmin-related myopathy. Nat Genet 1998; 20:92-5. [PMID: 9731540 DOI: 10.1038/1765] [Citation(s) in RCA: 789] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Desmin-related myopathies (DRM) are inherited neuromuscular disorders characterized by adult onset and delayed accumulation of aggregates of desmin, a protein belonging to the type III intermediate filament family, in the sarcoplasma of skeletal and cardiac muscles. In this paper, we have mapped the locus for DRM in a large French pedigree to a 26-cM interval in chromosome 11q21-23. This region contains the alphaB-crystallin gene (CRYAB), a candidate gene encoding a 20-kD protein that is abundant in lens and is also present in a number of non-ocular tissues, including cardiac and skeletal muscle. AlphaB-crystallin is a member of the small heat shock protein (shsp) family and possesses molecular chaperone activity. We identified an R120G missense mutation in CRYAB that co-segregates with the disease phenotype in this family. Muscle cell lines transfected with the mutant CRYAB cDNA showed intracellular aggregates that contain both desmin and alphaB-crystallin as observed in muscle fibers from DRM patients. These results are the first to identify a defect in a molecular chaperone as a cause for an inherited human muscle disorder.
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Affiliation(s)
- P Vicart
- Institut Pasteur, Paris, France.
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Austruy E, Candon S, Henry I, Gyapay G, Tournade MF, Mannens M, Callen D, Junien C, Jeanpierre C. Characterization of regions of chromosomes 12 and 16 involved in nephroblastoma tumorigenesis. Genes Chromosomes Cancer 1995; 14:285-94. [PMID: 8605117 DOI: 10.1002/gcc.2870140407] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
There are at least three loci involved in Wilms' tumor (WT) tumorigenesis: WT1 in 11p13, WT2 in 11p15.5, and WT3, as yet unmapped. A compilation of cytogenetic data published for 107 WT revealed that deletion of chromosome 16 and duplication of chromosome 12 occur as frequently as the well-documented 11p deletions. Allelic imbalance for chromosomes 16 and 12 was investigated in a series of 28 WT. By use of a large panel of restriction fragment length polymorphisms and (CA)n probes, we demonstrated loss of heterozygosity (LOH) for 16q in seven (25%) of the tumors. The whole length of 16q was involved in six of the tumors. Moreover, consistent with a previous report of 16q13 LOH in a sporadic WT and a constitutional breakpoint with a Beckwith-Wiedemann patient, we map a region of particular interest to between D16S308 and D16S320. The assumption that 16q LOH may be an early event was based on: 1) the detection of 16q LOH in one case of nephroblastomatosis; 2) the presence of a complete (clonal) 16q LOH in a tumor with partial (mosaic) 11p LOH; and 3) 16q LOH as the sole abnormality in one WT. By quantification of chromosome 12 allelic imbalance, we detected duplication in 18% of the total series and in 25% of the sporadic unilateral cases. The common region extended from the centromere to D12S7 in 12q21.1-q23. We also suggest that the various pathogenetically important loci are not equally involved in the different forms of WT and that their sequential involvement may differ.
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Affiliation(s)
- E Austruy
- INSERM U383, Université Paris V, Hôpital Necker-Enfants Malades, France
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