Dataset Information

NGS Sequencing Reveals New UCP1 Gene Variants Potentially Associated with MetS and/or T2DM Risk in the Polish Population-A Preliminary Study.

ABSTRACT: The number of people suffering from metabolic syndrome (MetS) including type 2 diabetes (T2DM), hypertension, and obesity increased over 10 times through the last 30 years and it is a severe public health concern worldwide. Uncoupling protein 1 (UCP1) is a mitochondrial carrier protein found only in brown adipose tissue involved in thermogenesis and energy expenditure. Several studies showed an association between UCP1 variants and the susceptibility to MetS, T2DM, and/or obesity in various populations; all these studies were, however, limited to a few selected polymorphisms. The present study aimed to search within the entire UCP1 gene for new variants potentially associated with MetS and/or T2DM risk. We performed NGS sequencing of the entire UCP1 gene in 59 MetS patients including 29 T2DM patients, and 36 controls using the MiSeq platform. An analysis of allele and genotype distribution revealed nine variations which seem to be interesting in the context of MetS and fifteen in the context of T2DM. Altogether, we identified 12 new variants, among which only rs3811787 was investigated previously by others. Thereby, NGS sequencing revealed new intriguing UCP1 gene variants potentially associated with MetS and/or T2DM risk in the Polish population.

SUBMITTER: Andrzejczak A

PROVIDER: S-EPMC10137642 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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NGS Sequencing Reveals New <i>UCP1</i> Gene Variants Potentially Associated with MetS and/or T2DM Risk in the Polish Population-A Preliminary Study.

Andrzejczak Anna A Witkowicz Agata A Kujawa Dorota D Skrypnik Damian D Szulińska Monika M Bogdański Paweł P Łaczmański Łukasz Ł Karabon Lidia L

Genes 20230324 4

The number of people suffering from metabolic syndrome (MetS) including type 2 diabetes (T2DM), hypertension, and obesity increased over 10 times through the last 30 years and it is a severe public health concern worldwide. Uncoupling protein 1 (UCP1) is a mitochondrial carrier protein found only in brown adipose tissue involved in thermogenesis and energy expenditure. Several studies showed an association between <i>UCP1</i> variants and the susceptibility to MetS, T2DM, and/or obesity in vario ...[more]

PMID: 37107547

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Project description:Osteoporosis in premenopausal women with intact gonadal function and no known secondary cause of bone loss is termed idiopathic osteoporosis (IOP). Women with IOP diagnosed in adulthood have profound bone structural deficits and often report adult and childhood fractures, and family history of osteoporosis. Some have very low bone formation rates (BFR/BS) suggesting osteoblast dysfunction. These features led us to investigate potential genetic etiologies of bone fragility. In 75 IOP women (aged 20-49) with low trauma fractures and/or very low BMD who had undergone transiliac bone biopsies, we performed Whole Exome Sequencing (WES) using our variant analysis pipeline to select candidate rare and novel variants likely to affect known disease genes. We ran rare-variant burden analyses on all genes individually and on phenotypically-relevant gene sets. For particular genes implicated in osteoporosis, we also assessed the frequency of all (including common) variants in subjects versus 6540 non-comorbid female controls. The variant analysis pipeline identified 4 women with 4 heterozygous variants in LRP5 and PLS3 that were considered to contribute to osteoporosis. All 4 women had adult fractures, and 3 women also had multiple fractures, childhood fractures and a family history of osteoporosis. Two women presented during pregnancy/lactation. In an additional 4 subjects, 4 different relevant Variants of Uncertain Significance (VUS) were detected in the genes FKBP10, SLC34A3, and HGD. Of the subjects with VUS, 2 had multiple adult fractures, childhood fractures, and presented during pregnancy/lactation, and 2 had nephrolithiasis. BFR/BS varied among the 8 subjects with identified variants; BFR/BS was quite low in those with variants that are likely to have adverse effects on bone formation. The analysis pipeline did not discover candidate variants in COL1A1, COL1A2, WNT, or ALPL. Although we found several novel and rare variants in LRP5, cases did not have an increased burden of common LRP5 variants compared to controls. Cohort-wide collapsing analysis did not reveal any novel disease genes with genome-wide significance for qualifying variants between controls and our 75 cases. In summary, WES revealed likely pathogenic variants or relevant VUS in 8 (11%) of 75 women with IOP. Notably, the genetic variants identified were consistent with the affected women's diagnostic evaluations that revealed histological evidence of low BFR/BS or biochemical evidence of increased bone resorption and urinary calcium excretion. These results, and the fact that the majority of the women had no identifiable genetic etiology, also suggest that the pathogenesis of and mechanisms leading to osteoporosis in this cohort are heterogeneous. Future research is necessary to identify both new genetic and non-genetic etiologies of early-onset osteoporosis.

Project description:PurposeThe aim of this study was to identify the molecular genetic basis of cone-rod dystrophy in 18 unrelated families of Polish origin. Cone-rod dystrophy is one of the inherited retinal dystrophies, which constitute a highly heterogeneous group of disorders characterized by progressive dysfunction of photoreceptors and retinal pigment epithelium (RPE) cells.MethodsThe study group was composed of four groups of patients representing different Mendelian inheritance of the disease: autosomal dominant (AD), autosomal recessive (AR), X-linked recessive (XL), and autosomal recessive or X-linked recessive (AR/XL). The combined molecular strategy included Sanger sequencing of the RPGR-ORF15 gene (three families with XL and three families with the AR/XL mode of inheritance), mutation-specific microarray analysis of the ABCA4 gene (five families with the AR mode of inheritance and two families with the AR/XL mode of inheritance), targeted next-generation sequencing (NGS) of inherited retinal disease-associated (IRD) genes (seven families with the AD mode of inheritance and five families with the AR mode of inheritance), and whole exome sequencing, performed in select families who had been mutation-negative in the analysis with the targeted NGS panel (one family with the AD mode of inheritance, one family with the AR mode of inheritance, and two families with the AR/XL mode of inheritance).ResultsBased on this combined strategy, we managed to identify potentially causative variants in seven out of 18 families with CRD. Five of these variants are novel: c.3142_3143dupAA, p.(Glu1049Argfs*41) in the RPGR-ORF15 gene, two variants: c.1612delT, p.(Trp538Glyfs*15) and c.2389dupG, p.(Ile798Hisfs*20) in the PROM1 gene in one family, c.592A>C, p.(Ser198Arg) in the PRPH2 gene and the variant c.1691A>G, p.(Asp564Gly) in the ATF6 gene that we have already reported to be pathogenic. NGS on the IRD panel allowed the molecular basis of CRD to be identified in four out of 14 families with a total detection rate of 38%. WES allowed identification of the molecular genetic basis of CRD in one family.ConclusionsThis is the first report on the spectrum of disease genes and pathogenic variants causing CRD in the Polish population. The study presents five novel variants identified in four genes and therefore, broadens the spectrum of probable pathogenic variants associated with CRD.

Dataset Information

NGS Sequencing Reveals New UCP1 Gene Variants Potentially Associated with MetS and/or T2DM Risk in the Polish Population-A Preliminary Study.

Publications

NGS Sequencing Reveals New <i>UCP1</i> Gene Variants Potentially Associated with MetS and/or T2DM Risk in the Polish Population-A Preliminary Study.

Similar Datasets

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