scholarly journals Functional Characterization of Clinically-Relevant Rare Variants in ABCG2 Identified in a Gout and Hyperuricemia Cohort

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 363 ◽  
Author(s):  
Toyoda ◽  
Mančíková ◽  
Krylov ◽  
Morimoto ◽  
Pavelcová ◽  
...  
Keyword(s):  
Genetic Risk ◽  
Rare Variants ◽  
Direct Sequencing ◽  
Functional Characterization ◽  
Cellular Proteins ◽  
European Descent ◽  
Primary Gout ◽  
Abcg2 Protein ◽  
Functional Analyses

ATP-binding cassette subfamily G member 2 (ABCG2) is a physiologically important urate transporter. Accumulating evidence demonstrates that congenital dysfunction of ABCG2 is an important genetic risk factor in gout and hyperuricemia; recent studies suggest the clinical significance of both common and rare variants of ABCG2. However, the effects of rare variants of ABCG2 on the risk of such diseases are not fully understood. Here, using a cohort of 250 Czech individuals of European descent (68 primary hyperuricemia patients and 182 primary gout patients), we examined exonic non-synonymous variants of ABCG2. Based on the results of direct sequencing and database information, we experimentally characterized nine rare variants of ABCG2: R147W (rs372192400), T153M (rs753759474), F373C (rs752626614), T421A (rs199854112), T434M (rs769734146), S476P (not annotated), S572R (rs200894058), D620N (rs34783571), and a three-base deletion K360del (rs750972998). Functional analyses of these rare variants revealed a deficiency in the plasma membrane localization of R147W and S572R, lower levels of cellular proteins of T153M and F373C, and null urate uptake function of T434M and S476P. Accordingly, we newly identified six rare variants of ABCG2 that showed lower or null function. Our findings contribute to deepening the understanding of ABCG2-related gout/hyperuricemia risk and the biochemical characteristics of the ABCG2 protein.

scholarly journals POS0352 ALLELIC VARIANTS IN THE ABCG2 GENE CAN LEAD TO HYPERURICEMIA AND GOUT

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 406.2-407
Author(s):  
K. Pavelcova ◽  
J. Bohata ◽  
B. Stiburkova
Keyword(s):  
Uric Acid ◽  
Rare Variants ◽  
Stop Codon ◽  
Functional Characterization ◽  
Premature Stop Codon ◽  
European Population ◽  
Allelic Variants ◽  
Abcg2 Protein ◽  
The Impact ◽  
Abcg2 Gene

Background:The level of uric acid is largely determined by the functions of urate transporters, which are located in the kidney and intestine. The ABCG2 protein is the major excretor of uric acid and its dysfunction may lead to the development of hyperuricemia and gout.Objectives:The aim of our study was to detect the occurrence and frequency of allelic variants in the ABCG2 gene that can lead to impaired function of the ABCG2 protein and to the development of hyperuricemia and gout.Methods:We examined allelic variants of ABCG2 using PCR amplification and Sanger sequencing of all coding regions and exon-intron boundaries in 359 patients with primary hyperuricemia and gout.Results:We found a rare in-frame deletion p.K360del and 15 missense variants, two of which were common (p.V12M, p.Q141K) and 13 were very rare (p.M71V, p.G74D, p.M131I, p.R147W, p.T153M, p.I242T, p.R236X, p.F373C, p.T421A, p.T434M, p.S476P, p.S572R, p.D620N). The p.R236X variant leads to a premature stop codon. The p.V12M variant probably has a protective effect against gout (minor allele frequency – MAF – in our cohort = 0,025 / MAF in the European population = 0,061), while the p.Q141K variant increases the risk of gout (MAF in our cohort = 0,213 / MAF in the European population = 0,094) (1). As for the rare variants, the p.R147W, p.T153M, p.F373C, p.T434M, p.S476P and p.S572R according to functional analyzes reduce the function of the ABCG2 protein (2). Based on in silico prediction, the impact on reduced function is expected for variants p.M71V, p.G74D, p.M131I, p.R147W, p.I242T, p.F373C, p.T434M, p.S476P and p.S572R.Conclusion:Our data suggest that the common variant p.Q141K and most of the rare variants in the ABCG2 gene affect the function of the ABCG2 urate transporter and are a genetic risk factor for hyperuricemia and gout.References:[1]Stiburkova B, et al. Functional non-synonymous variants of ABCG2 and gout risk. Rheumatology (Oxford). 2017 Nov 1; 56(11):1982-1992.[2]Toyoda Y, et al. Functional characterization of clinically-relevant rare variants in ABCG2 identified in a gout and hyperuricemia cohort. Cells. 2019 Apr 18;8(4).Acknowledgements:This study was supported by the project for conceptual development of research organization 00023728 (Institute of Rheumatology) and RVO VFN64165.Disclosure of Interests:None declared

scholarly journals Identification and functional characterization of NODAL rare variants in heterotaxy and isolated cardiovascular malformations

2008 ◽  
Vol 18 (5) ◽  
pp. 861-871 ◽  
Author(s):  
Bhagyalaxmi Mohapatra ◽  
Brett Casey ◽  
Hua Li ◽  
Trang Ho-Dawson ◽  
Liana Smith ◽  
...  
Keyword(s):  
Rare Variants ◽  
Functional Characterization ◽  
Cardiovascular Malformations

scholarly journals Functional characterization of the TAS2R38 bitter taste receptor for phenylthiocarbamide in colobine monkeys

2017 ◽  
Vol 13 (1) ◽  
pp. 20160834 ◽  
Author(s):  
Laurentia Henrieta Permita Sari Purba ◽  
Kanthi Arum Widayati ◽  
Kei Tsutsui ◽  
Nami Suzuki-Hashido ◽  
Takashi Hayakawa ◽  
...  
Keyword(s):  
Bitter Taste ◽  
Functional Characterization ◽  
Taste Receptor ◽  
Synonymous Mutations ◽  
Natural Toxins ◽  
Colobine Monkeys ◽  
Functional Analyses ◽  
G Protein Coupled

Bitterness perception in mammals is mostly directed at natural toxins that induce innate avoidance behaviours. Bitter taste is mediated by the G protein-coupled receptor TAS2R, which is located in taste cell membranes. One of the best-studied bitter taste receptors is TAS2R38, which recognizes phenylthiocarbamide (PTC). Here we investigate the sensitivities of TAS2R38 receptors to PTC in four species of leaf-eating monkeys (subfamily Colobinae). Compared with macaque monkeys (subfamily Cercopithecinae), colobines have lower sensitivities to PTC in behavioural and in vitro functional analyses. We identified four non-synonymous mutations in colobine TAS2R38 that are responsible for the decreased sensitivity of the TAS2R38 receptor to PTC observed in colobines compared with macaques. These results suggest that tolerance to bitterness in colobines evolved from an ancestor that was sensitive to bitterness as an adaptation to eating leaves.

scholarly journals Functional Characterization of TNNC1 Rare Variants Identified in Dilated Cardiomyopathy

2011 ◽  
Vol 286 (39) ◽  
pp. 34404-34412 ◽  
Author(s):  
Jose Renato Pinto ◽  
Jill D. Siegfried ◽  
Michelle S. Parvatiyar ◽  
Duanxiang Li ◽  
Nadine Norton ◽  
...  
Keyword(s):  
Dilated Cardiomyopathy ◽  
Rare Variants ◽  
Functional Characterization

T95. Functional Characterization of a DGKH Genetic Risk Variant for Bipolar Disorder in a Cell Model

2018 ◽  
Vol 83 (9) ◽  
pp. S165
Author(s):  
Sarah Kittel-Schneider ◽  
Viola Stella Palladino ◽  
Nadia Omega Cipta Subrata ◽  
Joyce Auer ◽  
Alicia Grein ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Genetic Risk ◽  
Cell Model ◽  
Functional Characterization ◽  
Risk Variant ◽  
Genetic Risk Variant ◽  
A Cell

scholarly journals Viral Ubiquitin and Ubiquitin-Like Deconjugases—Swiss Army Knives for Infection

Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1137
Author(s):  
Maria Grazia Masucci
Keyword(s):  
Life Cycle ◽  
Posttranslational Modifications ◽  
Viral Infections ◽  
Functional Characterization ◽  
Viral Life Cycle ◽  
Cellular Proteins ◽  
Antiviral Defense ◽  
Cellular Processes ◽  
Growing Body

Posttranslational modifications of cellular proteins by covalent conjugation of ubiquitin and ubiquitin-like polypeptides regulate numerous cellular processes that are captured by viruses to promote infection, replication, and spreading. The importance of these protein modifications for the viral life cycle is underscored by the discovery that many viruses encode deconjugases that reverse their functions. The structural and functional characterization of these viral enzymes and the identification of their viral and cellular substrates is providing valuable insights into the biology of viral infections and the host’s antiviral defense. Given the growing body of evidence demonstrating their key contribution to pathogenesis, the viral deconjugases are now recognized as attractive targets for the design of novel antiviral therapeutics.

scholarly journals New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs

2020 ◽  
Vol 48 (14) ◽  
pp. 7700-7711 ◽  
Author(s):  
Shoudong Zhang ◽  
Runsheng Li ◽  
Li Zhang ◽  
Shengjie Chen ◽  
Min Xie ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Transcription Initiation ◽  
Direct Sequencing ◽  
Functional Characterization ◽  
Read Length ◽  
Long Distance ◽  
Transcript Isoforms ◽  
Fusion Transcripts ◽  
Novel Transcript

Abstract Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current ‘RNA-sequencing’ technologies produce a relatively short read length and demand a reverse-transcription step, preventing effective characterization of transcriptome complexity. Here, we performed Direct RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been substantially under-estimated. The ONT direct RNA sequencing identified novel transcript isoforms at both the vegetative (14-day old seedlings, stage 1.04) and reproductive stages (stage 6.00–6.10) of development. Using in-house software called TrackCluster, we determined alternative transcription initiation (ATI), alternative polyadenylation (APA), alternative splicing (AS), and fusion transcripts. More than 38 500 novel transcript isoforms were identified, including six categories of fusion-transcripts that may result from differential RNA processing mechanisms. Aided by the Tombo algorithm, we found an enrichment of m5C modifications in the mobile mRNAs, consistent with a recent finding that m5C modification in mRNAs is crucial for their long-distance movement. In summary, ONT DRS offers an advantage in the identification and functional characterization of novel RNA isoforms and RNA base modifications, significantly improving annotation of the A. thaliana genome.

scholarly journals Functional Characterization of 21 Rare Allelic CYP1A2 Variants Identified in a Population of 4773 Japanese Individuals by Assessing Phenacetin O-Deethylation

2021 ◽  
Vol 11 (8) ◽  
pp. 690
Author(s):  
Masaki Kumondai ◽  
Evelyn Marie Gutiérrez Rico ◽  
Eiji Hishinuma ◽  
Yuya Nakanishi ◽  
Shuki Yamazaki ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Protein Function ◽  
Rare Variants ◽  
Functional Characterization ◽  
Three Dimensional ◽  
Additional Information ◽  
Metabolic Reactions ◽  
Underlying Mechanisms ◽  
Cytochrome Content

Cytochrome P450 1A2 (CYP1A2), which accounts for approximately 13% of the total hepatic cytochrome content, catalyzes the metabolic reactions of approximately 9% of frequently used drugs, including theophylline and olanzapine. Substantial inter-individual differences in enzymatic activity have been observed among patients, which could be caused by genetic polymorphisms. Therefore, we functionally characterized 21 novel CYP1A2 variants identified in 4773 Japanese individuals by determining the kinetic parameters of phenacetin O-deethylation. Our results showed that most of the evaluated variants exhibited decreased or no enzymatic activity, which may be attributed to potential structural alterations. Notably, the Leu98Gln, Gly233Arg, Ser380del Gly454Asp, and Arg457Trp variants did not exhibit quantifiable enzymatic activity. Additionally, three-dimensional (3D) docking analyses were performed to further understand the underlying mechanisms behind variant pharmacokinetics. Our data further suggest that despite mutations occurring on the protein surface, accumulating interactions could result in the impairment of protein function through the destabilization of binding regions and changes in protein folding. Therefore, our findings provide additional information regarding rare CYP1A2 genetic variants and how their underlying effects could clarify discrepancies noted in previous phenotypical studies. This would allow the improvement of personalized therapeutics and highlight the importance of identifying and characterizing rare variants.

scholarly journals Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing

2020 ◽  
Author(s):  
Jordi Silvestre-Ryan ◽  
Ian Holmes
Keyword(s):  
Neural Network ◽  
Error Rate ◽  
Rare Variants ◽  
Direct Sequencing ◽  
Consensus Algorithm ◽  
Dna Duplexes ◽  
Oxford Nanopore ◽  
Median Error ◽  
Improving Accuracy

AbstractNanopore technology allows for direct sequencing of individual DNA duplexes. However, its higher error rate compared to other sequencing methods has limited its application in situations where deep coverage is unavailable, such as detection of rare variants or characterization of highly polymorphic samples. In principle, 2X coverage is available even for single duplexes, using Oxford Nanopore Technologies’ 1D2 protocol or related methods which sequence both strands of the duplex consecutively. Using both strands should improve accuracy; however, most neural network basecaller architectures are designed to operate on single strands. We have developed a general approach for improving accuracy of 1D2 and related protocols by finding the consensus of two neural network basecallers, by combining a constrained profile-profile alignment with a heuristic variant of beam search. When run on a basecalling neural network we trained, our consensus algorithm improves median basecall accuracy from 86.2% (for single-read decoding) to 92.1% (for pair decoding). Our software can readily be adapted to work with the output of other basecallers, such as the recently released Bonito basecaller. Although Bonito operates only on individual strands and was not designed to leverage the 1D2 protocol, our method lifts its median accuracy from 93.3% to 97.7%, more than halving the median error rate. This surpasses the maximum accuracy achievable with Guppy, an alternate basecaller which was designed to include pair decoding of 1D2 reads. Our software PoreOver, including both our neural network basecaller and our consensus pair decoder (which can be separably applied to improve other basecallers), is implemented in Python 3 and C++11 and is freely available at https://github.com/jordisr/poreover.

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