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Thote V, Dinesh S, Sharma S. Prediction of deleterious non-synonymous SNPs of human MDC1 gene: an in silico approach. Syst Biol Reprod Med 2024; 70:101-112. [PMID: 38630598 DOI: 10.1080/19396368.2024.2325699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/24/2024] [Indexed: 04/19/2024]
Abstract
MDC1 (Mediator of DNA damage Checkpoint protein 1) functions to facilitate the localization of numerous DNA damage response (DDR) components to DNA double-strand break sites. MDC1 is an integral component in preserving genomic stability and appropriate DDR regulation. There haven't been systematic investigations of MDC1 mutations that induce cancer and genomic instability. Variations in nsSNPs have the potential to modify the protein chemistry and their function. Describing functional SNPs in disease-associated genes presents a significant conundrum for investigators, it is possible to assess potential functional SNPs before conducting larger population examinations. Multiple sequences and structure-based bioinformatics strategies were implemented in the current in-silico investigation to discern potential nsSNPs of the MDC1 genes. The nsSNPs were identified with SIFT, SNAP2, Align GVGD, PolyPhen-2, and PANTHER, and their stability was determined with MUpro. The conservation, solvent accessibility, and structural effects of the mutations were identified with ConSurf, NetSurfP-2.0, and SAAFEC-SEQ respectively. Cancer-related analysis of the nsSNPs was conducted using cBioPortal and TCGA web servers. The present study appraised five nsSNPs (P1426T, P69S, P194R, P203L, and H131Y) as probably mutilating due to their existence in highly conserved regions and propensity to deplete protein stability. The nsSNPs P194R, P203L, and H131Y were concluded as deleterious and possibly damaging from the 5 prediction tools. The functional nsSNP P194R mutation is associated with skin cutaneous melanoma while no significant records were found for other nsSNPs. The present study concludes that the highly deleterious P194R mutations can potentially induce genomic instability and contribute to various cancers' pathogenesis. Developing drugs targeting these mutations can undoubtedly be advantageous in large population-based studies, particularly in the development of precision medicine.
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Affiliation(s)
| | - Susha Dinesh
- Department of Bioinformatics, BioNome, Bengaluru, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bengaluru, India
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2
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Kojom Foko LP, Hawadak J, Eboumbou Moukoko CE, Das A, Singh V. Genetic analysis of the circumsporozoite gene in Plasmodium falciparum isolates from Cameroon: Implications for efficacy and deployment of RTS,S/AS01 vaccine. Gene 2024; 927:148744. [PMID: 38964492 DOI: 10.1016/j.gene.2024.148744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Current understanding of genetic polymorphisms and natural selection in Plasmodium falciparum circumsporozoite (PfCSP), the leading malaria vaccine, is crucial for the development of next-generation vaccines, and such data is lacking in Africa. Blood samples were collected among Plasmodium-infected individuals living in four Cameroonian areas (Douala, Maroua, Mayo-Oulo, Pette). DNA samples were amplified using nested PCR protocols, sequenced, and BLASTed. Single nucleotide polymorphisms (SNPs) were analysed in each PfCSP region, and their impact on PfCSP function/structure was predicted in silico. The N-terminal region showed a limited polymorphism with four haplotypes, and three novel SNPs (N68Y, R87W, K93E) were found. Thirty-five haplotypes were identified in the central region, with several variants (e.g., NVNP and KANP). The C-terminal region was also highly diverse, with 25 haplotypes and eight novel SNPs (N290D, N308I, S312G, K317A, V344I, D356E, E357L, D359Y). Most polymorphic codon sites were mainly observed in the Th2R subregion in isolates from Douala and Pette. The codon site 321 was under episodic positive selection. One novel (E357L) and three known (K322I, G349D, D359Y) SNPs show an impact on function/structure. This study showed extensive genetic diversity with geographical patterns and evidence of the selection of Cameroonian PfCSP central and C-terminal regions.
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Affiliation(s)
| | - Joseph Hawadak
- Parasite & Host Biology Group, National Institute of Malaria Research, New-Delhi, India
| | - Carole Else Eboumbou Moukoko
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, The University of Douala, Cameroon; Malaria Research Unit, Centre Pasteur Cameroon, Yaoundé, Cameroon; Laboratory of Parasitology, Mycology and Virology, Postgraduate Training Unit for Health Sciences, Postgraduate School for Pure and Applied Sciences, The University of Douala, Cameroon
| | - Aparup Das
- Division of Vector Borne Diseases, National Institute of Research in Tribal Health, Madhya Pradesh, India
| | - Vineeta Singh
- Parasite & Host Biology Group, National Institute of Malaria Research, New-Delhi, India; Academy of Scientific and Innovative Research, Ghaziabad, India.
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3
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Okutman Ö, Gürbüz AS, Salvarci A, Büyük U, Ruso H, Gürgan T, Tarabeux J, Leuvrey AS, Nourisson E, Lang C, Muller J, Viville S. Evaluation of an Updated Gene Panel as a Diagnostic Tool for Both Male and Female Infertility. Reprod Sci 2024; 31:2309-2317. [PMID: 38664359 DOI: 10.1007/s43032-024-01553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/02/2024] [Indexed: 07/31/2024]
Abstract
In recent years, an increasing number of genes associated with male and female infertility have been identified. The genetics of infertility is no longer limited to the analysis of karyotypes or specific genes, and it is now possible to analyse several dozen infertility genes simultaneously. Here, we present the diagnostic activity over the past two years including 140 patients (63 women and 77 men). Targeted sequencing revealed causative variants in 17 patients, representing an overall diagnostic rate of 12.1%, with prevalence rates in females and males of 11% and 13%, respectively. The gene-disease relationship (GDR) was re-evaluated for genes due to the addition of new patients and/or variants in the actual study. Five genes changed categories: two female genes (MEIOB and TBPL2) moved from limited to moderate; two male genes (SOHLH1 and GALNTL5) moved from no evidence to strong and from limited to moderate; and SEPTIN12, which was unable to classify male infertility, was reclassified as limited. Many infertility genes have yet to be identified. With the increasing integration of genetics in reproductive medicine, the scope of intervention extends to include other family members, in addition to individual patients or couples. Genetic counselling consultations and appropriate staffing will need to be established in fertility centres. Trial registration number: Not applicable.
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Affiliation(s)
- Özlem Okutman
- Service de Gynécologie-Obstetrique, Clinique de Fertilité, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (H.U.B), Hôpital Erasme, Route de Lennik, 808, 1070, Brussels, Belgium.
| | | | | | - Umut Büyük
- Department of Molecular Biology and Genetics, Institute of Graduate Studies in Sciences, Istanbul University, Istanbul, Turkey
| | - Halil Ruso
- Gürgan Clinic Women's Health and IVF Centre, Ankara, Turkey
- Faculty of Medicine, Department of Histology and Embryology, Gazi University, Ankara, Turkey
| | - Timur Gürgan
- Gürgan Clinic Women's Health and IVF Centre, Ankara, Turkey
- Department of Obstetrics and Gynecology, Bahçeşehir University School of Medicine, Istanbul, Turkey
| | - Julien Tarabeux
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Anne-Sophie Leuvrey
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Elsa Nourisson
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Cécile Lang
- Laboratoire de Diagnostic Génétique, Unité de Génétique de L'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg, INSERM UMR 1112, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale Appliquée Au Diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Stephane Viville
- Laboratoire de Diagnostic Génétique, Unité de Génétique de L'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg, INSERM UMR 1112, Strasbourg, France
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4
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Kamal MM, Islam MN, Rabby MG, Zahid MA, Hasan MM. In Silico Functional and Structural Analysis of Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in Human Paired Box 4 Gene. Biochem Genet 2024; 62:2975-2998. [PMID: 38062275 DOI: 10.1007/s10528-023-10589-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 11/06/2023] [Indexed: 07/31/2024]
Abstract
In human genome, members of Paired box (PAX) transcription factor family are highly sequence-specific DNA-binding proteins. Among PAX gene family members, PAX4 gene has significant role in growth, proliferation, differentiation, and insulin secretion of pancreatic β-cells. Single nucleotide polymorphisms (SNPs) in PAX4 gene progress in the pathogenesis of various human diseases. Hence, the molecular mechanism of how these SNPs in PAX4 gene significantly progress diseases pathogenesis needs to be elucidated. For the reason, a series of bioinformatic analyzes were done to identify the SNPs of PAX4 gene that contribute in diseases pathogenesis. From the analyzes, 4145 SNPs (rsIDs) in PAX4 gene were obtained, where, 362 missense (8.73%), 169 synonymous (4.08%), and 2323 intron variants (56.04%). The rest SNPs were unspecified. Among the 362 missense variants, 118 nsSNPs were found as deleterious in SIFT analysis. Among those, 25 nsSNPs were most probably damaging and 23 were deleterious as observed in PolyPhen-2 and PROVEAN analyzes, respectively. Following all analyzes, 14 nsSNPs (rs149708455, rs115887120, rs147279315, rs35155575, rs370095957, rs373939873, rs145468905, rs121917718, rs2233580, rs3824004, rs372751660, rs369459316, rs375472849, rs372497946) were common and observed as deleterious, probably damaging, affective and diseases associated. Following structural analyzes, 11 nsSNPs guided proteins were found as most unstable and highly conserved. Among these, R20W, R39Q, R45Q, R60H, G65D, and A223D mutated proteins were highly harmful. Hence, the results from above-mentioned integrated comprehensive bioinformatic analyzes guide how different nsSNPs in PAX4 gene alter structural and functional characteristics of the protein that might progress diseases pathogenesis in human including type 2 diabetes.
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Affiliation(s)
- Md Mostafa Kamal
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Numan Islam
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Food Engineering, North Pacific International University of Bangladesh, Dhaka, Bangladesh
| | - Md Golam Rabby
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Ashrafuzzaman Zahid
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh.
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5
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Cirulli ET, Schiabor Barrett KM, Bolze A, Judge DP, Pawloski PA, Grzymski JJ, Lee W, Washington NL. A power-based sliding window approach to evaluate the clinical impact of rare genetic variants in the nucleotide sequence or the spatial position of the folded protein. HGG ADVANCES 2024; 5:100284. [PMID: 38509709 PMCID: PMC11004801 DOI: 10.1016/j.xhgg.2024.100284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Systematic determination of novel variant pathogenicity remains a major challenge, even when there is an established association between a gene and phenotype. Here we present Power Window (PW), a sliding window technique that identifies the impactful regions of a gene using population-scale clinico-genomic datasets. By sizing analysis windows on the number of variant carriers, rather than the number of variants or nucleotides, statistical power is held constant, enabling the localization of clinical phenotypes and removal of unassociated gene regions. The windows can be built by sliding across either the nucleotide sequence of the gene (through 1D space) or the positions of the amino acids in the folded protein (through 3D space). Using a training set of 350k exomes from the UK Biobank (UKB), we developed PW models for well-established gene-disease associations and tested their accuracy in two independent cohorts (117k UKB exomes and 65k exomes sequenced at Helix in the Healthy Nevada Project, myGenetics, or In Our DNA SC studies). The significant models retained a median of 49% of the qualifying variant carriers in each gene (range 2%-98%), with quantitative traits showing a median effect size improvement of 66% compared with aggregating variants across the entire gene, and binary traits' odds ratios improving by a median of 2.2-fold. PW showcases that electronic health record-based statistical analyses can accurately distinguish between novel coding variants in established genes that will have high phenotypic penetrance and those that will not, unlocking new potential for human genomics research, drug development, variant interpretation, and precision medicine.
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Affiliation(s)
| | | | - Alexandre Bolze
- Helix, 101 S Ellsworth Ave Suite 350, San Mateo, CA 94401, USA
| | - Daniel P Judge
- Division of Cardiology, Medical University of South Carolina, 30 Courtenay Drive, MSC 592, Charleston, SC 29425, USA
| | | | - Joseph J Grzymski
- University of Nevada, 2215 Raggio Pkwy, Reno, NV 89512, USA; Renown Institute for Health Innovation, Reno, NV 89512, USA
| | - William Lee
- Helix, 101 S Ellsworth Ave Suite 350, San Mateo, CA 94401, USA
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6
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Bloks NG, Harissa Z, Mazzini G, Adkar SS, Dicks AR, Hajmousa G, Steward N, Koning RI, Mulder A, de Koning BBR, Kloppenburg M, de Almeida RC, Ramos YF, Guilak F, Meulenbelt I. A Damaging COL6A3 Variant Alters the MIR31HG-Regulated Response of Chondrocytes in Neocartilage Organoids to Hyperphysiologic Mechanical Loading. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400720. [PMID: 39021299 DOI: 10.1002/advs.202400720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 06/28/2024] [Indexed: 07/20/2024]
Abstract
The pericellular matrix (PCM), with its hallmark proteins collagen type VI (COLVI) and fibronectin (FN), surrounds chondrocytes and is critical in transducing the biomechanical cues. To identify genetic variants that change protein function, exome sequencing is performed in a patient with symptomatic OA at multiple joint sites. A predicted damaging variant in COL6A3 is identified and introduced by CRISPR-Cas9 genome engineering in two established human induced pluripotent stem cell-derived in-vitro neocartilage organoid models. The downstream effects of the COL6A3 variant on the chondrocyte phenotypic state are studied by a multi-omics (mRNA and lncRNA) approach in interaction with hyper-physiological mechanical loading conditions. The damaging variant in COL6A3 results in significantly lower binding between the PCM proteins COLVI and FN and provokes an osteoarthritic chondrocyte state. By subsequently exposing the neocartilage organoids to hyperphysiological mechanical stress, it is demonstrated that the COL6A3 variant in chondrocytes abolishes the characteristic inflammatory signaling response after mechanical loading with PTGS2, PECAM1, and ADAMTS5, as central genes. Finally, by integrating epigenetic regulation, the lncRNA MIR31HG is identified as key regulator of the characteristic inflammatory signaling response to mechanical loading.
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Affiliation(s)
- Niek Gc Bloks
- Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Zainab Harissa
- Washington University, Saint Louis, MO, 63110, USA
- Shriners Hospitals for Children, Saint Louis, MO, 63110, USA
| | - Giorgia Mazzini
- Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Shaunak S Adkar
- Washington University, Saint Louis, MO, 63110, USA
- Shriners Hospitals for Children, Saint Louis, MO, 63110, USA
| | - Amanda R Dicks
- Washington University, Saint Louis, MO, 63110, USA
- Shriners Hospitals for Children, Saint Louis, MO, 63110, USA
| | | | - Nancy Steward
- Washington University, Saint Louis, MO, 63110, USA
- Shriners Hospitals for Children, Saint Louis, MO, 63110, USA
| | - Roman I Koning
- Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Aat Mulder
- Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | | | | | | | - Yolande Fm Ramos
- Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Farshid Guilak
- Washington University, Saint Louis, MO, 63110, USA
- Shriners Hospitals for Children, Saint Louis, MO, 63110, USA
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7
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Ali I, Ali H, Unar A, Rahim F, Khan K, Dil S, Abbas T, Hussain A, Zeb A, Zubair M, Zhang H, Ma H, Jiang X, Khan MA, Xu B, Shah W, Shi Q. A novel homozygous missense TTC12 variant identified in an infertile Pakistani man with severe oligoasthenoteratozoospermia and primary ciliary dyskinesia. Mol Genet Genomics 2024; 299:69. [PMID: 38992144 DOI: 10.1007/s00438-024-02161-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/23/2024] [Indexed: 07/13/2024]
Abstract
TTC12 is a cytoplasmic and centromere-localized protein that plays a role in the proper assembly of dynein arm complexes in motile cilia in both respiratory cells and sperm flagella. This finding underscores its significance in cellular motility and function. However, the wide role of TTC12 in human spermatogenesis-associated primary ciliary dyskinesia (PCD) still needs to be elucidated. Whole-exome sequencing (WES) and Sanger sequencing were performed to identify potentially pathogenic variants causing PCD and multiple morphological abnormalities of sperm flagella (MMAF) in an infertile Pakistani man. Diagnostic imaging techniques were used for PCD screening in the patient. Real-time polymerase chain reaction (RT‒PCR) was performed to detect the effect of mutations on the mRNA abundance of the affected genes. Papanicolaou staining and scanning electron microscopy (SEM) were carried out to examine sperm morphology. Transmission electron microscopy (TEM) was performed to examine the ultrastructure of the sperm flagella, and the results were confirmed by immunofluorescence staining. Using WES and Sanger sequencing, a novel homozygous missense variant (c.C1069T; p.Arg357Trp) in TTC12 was identified in a patient from a consanguineous family. A computed tomography scan of the paranasal sinuses confirmed the symptoms of the PCD. RT-PCR showed a decrease in TTC12 mRNA in the patient's sperm sample. Papanicolaou staining, SEM, and TEM analysis revealed a significant change in shape and a disorganized axonemal structure in the sperm flagella of the patient. Immunostaining assays revealed that TTC12 is distributed throughout the flagella and is predominantly concentrated in the midpiece in normal spermatozoa. In contrast, spermatozoa from patient deficient in TTC12 showed minimal staining intensity for TTC12 or DNAH17 (outer dynein arms components). This could lead to MMAF and result in male infertility. This novel TTC12 variant not only illuminates the underlying genetic causes of male infertility but also paves the way for potential treatments targeting these genetic factors. This study represents a significant advancement in understanding the genetic basis of PCD-related infertility.
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Affiliation(s)
- Imtiaz Ali
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Haider Ali
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Ahsanullah Unar
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Fazal Rahim
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Khalid Khan
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Sobia Dil
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Tanveer Abbas
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Ansar Hussain
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Aurang Zeb
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Muhammad Zubair
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Huan Zhang
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Hui Ma
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaohua Jiang
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Bo Xu
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China.
| | - Wasim Shah
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China.
| | - Qinghua Shi
- Institute of Health and Medicine Division of Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Hefei Comprehensive National Science CenterFirst Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at MicroscaleBiomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China.
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8
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Dereli O, Kuru N, Akkoyun E, Bircan A, Tastan O, Adebali O. PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting. Mol Biol Evol 2024; 41:msae136. [PMID: 38934805 PMCID: PMC11251492 DOI: 10.1093/molbev/msae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/30/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Most algorithms that are used to predict the effects of variants rely on evolutionary conservation. However, a majority of such techniques compute evolutionary conservation by solely using the alignment of multiple sequences while overlooking the evolutionary context of substitution events. We had introduced PHACT, a scoring-based pathogenicity predictor for missense mutations that can leverage phylogenetic trees, in our previous study. By building on this foundation, we now propose PHACTboost, a gradient boosting tree-based classifier that combines PHACT scores with information from multiple sequence alignments, phylogenetic trees, and ancestral reconstruction. By learning from data, PHACTboost outperforms PHACT. Furthermore, the results of comprehensive experiments on carefully constructed sets of variants demonstrated that PHACTboost can outperform 40 prevalent pathogenicity predictors reported in the dbNSFP, including conventional tools, metapredictors, and deep learning-based approaches as well as more recent tools such as AlphaMissense, EVE, and CPT-1. The superiority of PHACTboost over these methods was particularly evident in case of hard variants for which different pathogenicity predictors offered conflicting results. We provide predictions of 215 million amino acid alterations over 20,191 proteins. PHACTboost is available at https://github.com/CompGenomeLab/PHACTboost. PHACTboost can improve our understanding of genetic diseases and facilitate more accurate diagnoses.
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Affiliation(s)
- Onur Dereli
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Nurdan Kuru
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Emrah Akkoyun
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
- Network Technologies Department, TÜBİTAK-ULAKBİM Turkish Academic Network and Information Center, Ankara 06530, Turkey
| | - Aylin Bircan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Oznur Tastan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Ogün Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
- Biological Sciences, TÜBİTAK Research Institute for Fundamental Sciences, Gebze 41470, Turkey
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9
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Bardey F, Rieck L, Spira D, März W, Binner P, Schwab S, Kleber ME, Danyel M, Barkowski R, Bobbert T, Spranger J, Steinhagen-Thiessen E, Demuth I, Kassner U. Clinical characterization and mutation spectrum of patients with hypertriglyceridemia in a German outpatient clinic. J Lipid Res 2024:100589. [PMID: 38969064 DOI: 10.1016/j.jlr.2024.100589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/13/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Severe hypertriglyceridemia (HTG) has predominantly multifactorial causes (MCS). Yet a small subset of patients have the monogenetic form (FCS). It remains a challenge to distinguish patients clinically, since decompensated MCS might mimic FCS´s severity. Aim of the current study was to determine clinical criteria that could sufficiently distinguish both forms as well as to apply the FCS score proposed by Moulin and colleagues. METHODS We retrospectively studied 72 patients who presented with severe HTG in our clinic during a time span of seven years and received genetic testing. We classified genetic variants (ACMG-criteria), followed by genetic categorization into MCS or FCS. Clinical data were gathered from the medical records and the FCS score was calculated for each patient. RESULTS Molecular genetic screening revealed eight FCS patients and 64 MCS patients. Altogether, we found 13 pathogenic variants of which four have not been described before. The FCS patients showed a significantly higher median triglyceride level compared to the MCS. The FCS score yielded a sensitivity of 75% and a specificity of 93.7% in our cohort, and significantly differentiated between the FCS and MCS group (p<0.001). CONCLUSIONS In our cohort we identified several variables that significantly differentiated FCS from MCS. The FCS score performed similar to the original study by Moulin, thereby further validating the discriminatory power of the FCS score in an independent cohort.
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Affiliation(s)
- Frieda Bardey
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Lorenz Rieck
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dominik Spira
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Winfried März
- Synlab Academy, P5, 7, 68167 Mannheim, Germany; Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbrugger Platz 15, 8036 Graz
| | - Priska Binner
- Synlab Center of Human Genetics, Harrlachweg 1, 68163 Mannheim, Germany
| | - Stefanie Schwab
- Synlab Center of Human Genetics, Harrlachweg 1, 68163 Mannheim, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; Synlab Center of Human Genetics, Harrlachweg 1, 68163 Mannheim, Germany
| | - Magdalena Danyel
- Berlin Institute of Health (BIH), Berlin, Germany; Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Rasmus Barkowski
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Thomas Bobbert
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Joachim Spranger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Elisabeth Steinhagen-Thiessen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
| | - Ilja Demuth
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany; Charité - Universitätsmedizin Berlin, BCRT - Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.
| | - Ursula Kassner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Endocrinology and Metabolic Diseases (including Division of Lipid Metabolism), Augustenburger Platz 1, 13353 Berlin, Germany
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10
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Höfler T, Nascimento MM, Zeitlow M, Kim JY, Trimpert J. Evolutionary Dynamics of Accelerated Antiviral Resistance Development in Hypermutator Herpesvirus. Mol Biol Evol 2024; 41:msae119. [PMID: 38879872 PMCID: PMC11226790 DOI: 10.1093/molbev/msae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/09/2024] [Accepted: 06/12/2024] [Indexed: 07/07/2024] Open
Abstract
Antiviral therapy is constantly challenged by the emergence of resistant pathogens. At the same time, experimental approaches to understand and predict resistance are limited by long periods required for evolutionary processes. Here, we present a herpes simplex virus 1 mutant with impaired proofreading capacity and consequently elevated mutation rates. Comparing this hypermutator to parental wild type virus, we study the evolution of antiviral drug resistance in vitro. We model resistance development and elucidate underlying genetic changes against three antiviral substances. Our analyzes reveal no principle difference in the evolutionary behavior of both viruses, adaptive processes are overall similar, however significantly accelerated for the hypermutator. We conclude that hypermutator viruses are useful for modeling adaptation to antiviral therapy. They offer the benefit of expedited adaptation without introducing apparent bias and can therefore serve as an accelerator to predict natural evolution.
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Affiliation(s)
- Thomas Höfler
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Mariana Mara Nascimento
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Michaela Zeitlow
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Ji Yoon Kim
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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11
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Tian R, Zhang Y, Kang H, Zhang F, Jin Z, Wang J, Zhang P, Zhou X, Lanyon JM, Sneath HL, Woolford L, Fan G, Li S, Seim I. Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 2024; 15:5568. [PMID: 38956050 PMCID: PMC11219930 DOI: 10.1038/s41467-024-49769-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Yaolei Zhang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Zhang
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Zhihong Jin
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Jiahao Wang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Janet M Lanyon
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Helen L Sneath
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Lucy Woolford
- School of Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, Australia
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China.
- BGI Research, Shenzhen, 518083, China.
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China.
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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12
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Zaka A, Yousaf M, Shahzad S, Rao HZ, Foo JN, Siddiqi S. Structural and functional insights into a novel homozygous missense pathogenic variant in CUL7 identified in consanguineous Pakistani family. J Biomol Struct Dyn 2024; 42:5092-5103. [PMID: 37345548 DOI: 10.1080/07391102.2023.2224889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/08/2023] [Indexed: 06/23/2023]
Abstract
3M syndrome is a rare genetic familial disorder characterized by short stature, growth retardation, facial dysmorphism, skeletal abnormalities, fleshy protruding heels, and normal intelligence, caused by mutations in the CUL7, OBSL1 and CCDC8 genes. In the present study, a novel homozygous missense variant of CUL7 (NP_001161842.1, c.4493T > C, p.L1498P) has been identified in a consanguineous Pakistani family by whole exome sequencing. In silico structural evaluation, molecular docking and simulation studies of mutant CUL7 provides substantial evidence about its crucial role in the progression of discussed ailment. The newly discovered variant significantly altered the protein's three dimensional structure, leading to abnormal interaction with binding proteins. This computational and experimental investigation provides useful information to drug developers for the synthesis of novel therapeutics against the discussed ailment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayesha Zaka
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
| | - Maha Yousaf
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Shaheen Shahzad
- Genomics Research Lab, Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Hadi Zahid Rao
- Department of Oral & Maxillofacial Surgery, Bahria University Medical and Dental College Karachi, Pakistan
| | - Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Saima Siddiqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
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13
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Kakar N, Rehman FU, Kaur R, Bhavani GS, Goyal M, Shah H, Kaur K, Sodhi KS, Kubisch C, Borck G, Panigrahi I, Girisha KM, Kornak U, Spielmann M. Multi-gene panel sequencing in highly consanguineous families and patients with congenital forms of skeletal dysplasias. Clin Genet 2024; 106:47-55. [PMID: 38378010 DOI: 10.1111/cge.14509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024]
Abstract
Skeletal dysplasias (SKDs) are a heterogeneous group of more than 750 genetic disorders characterized by abnormal development, growth, and maintenance of bones or cartilage in the human skeleton. SKDs are often caused by variants in early patterning genes and in many cases part of multiple malformation syndromes and occur in combination with non-skeletal phenotypes. The aim of this study was to investigate the underlying genetic cause of congenital SKDs in highly consanguineous Pakistani families, as well as in sporadic and familial SKD cases from India using multigene panel sequencing analysis. Therefore, we performed panel sequencing of 386 bone-related genes in 7 highly consanguineous families from Pakistan and 27 cases from India affected with SKDs. In the highly consanguineous families, we were able to identify the underlying genetic cause in five out of seven families, resulting in a diagnostic yield of 71%. Whereas, in the sporadic and familial SKD cases, we identified 12 causative variants, corresponding to a diagnostic yield of 44%. The genetic heterogeneity in our cohorts was very high and we were able to detect various types of variants, including missense, nonsense, and frameshift variants, across multiple genes known to cause different types of SKDs. In conclusion, panel sequencing proved to be a highly effective way to decipher the genetic basis of SKDs in highly consanguineous families as well as sporadic and or familial cases from South Asia. Furthermore, our findings expand the allelic spectrum of skeletal dysplasias.
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Affiliation(s)
- Naseebullah Kakar
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Fazal Ur Rehman
- Department of Pathology, Bolan Medical College, Quetta, Pakistan
| | - Ramandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Manisha Goyal
- Pediatrics Genetic & Research Laboratory, Department of Pediatrics, Lok Nayak Hospital, New Delhi, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Karandeep Kaur
- Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | | | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guntram Borck
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | | | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Malte Spielmann
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, University of Lübeck and University of Kiel, Lübeck, Germany
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14
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Herrera-Pariente C, Bonjoch L, Muñoz J, Fernàndez G, Soares de Lima Y, Mahmood R, Cuatrecasas M, Ocaña T, Lopez-Prades S, Llargués-Sistac G, Domínguez-Rovira X, Llach J, Luzko I, Díaz-Gay M, Lazaro C, Brunet J, Castillo-Manzano C, García-González MA, Lanas A, Carrillo M, Hernández San Gil R, Quintero E, Sala N, Llort G, Aguilera L, Carot L, Diez-Redondo P, Jover R, Ramon Y Cajal T, Cubiella J, Castells A, Balaguer F, Bujanda L, Castellví-Bel S, Moreira L. CTNND1 is involved in germline predisposition to early-onset gastric cancer by affecting cell-to-cell interactions. Gastric Cancer 2024; 27:747-759. [PMID: 38796558 PMCID: PMC11193828 DOI: 10.1007/s10120-024-01504-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/20/2024] [Indexed: 05/28/2024]
Abstract
BACKGROUND CDH1 and CTNNA1 remain as the main genes for hereditary gastric cancer. However, they only explain a small fraction of gastric cancer cases with suspected inherited basis. In this study, we aimed to identify new hereditary genes for early-onset gastric cancer patients (EOGC; < 50 years old). METHODS After germline exome sequencing in 20 EOGC patients and replication of relevant findings by gene-panel sequencing in an independent cohort of 152 patients, CTNND1 stood out as an interesting candidate gene, since its protein product (p120ctn) directly interacts with E-cadherin. We proceeded with functional characterization by generating two knockout CTNND1 cellular models by gene editing and introducing the detected genetic variants using a lentiviral delivery system. We assessed β-catenin and E-cadherin levels, cell detachment, as well as E-cadherin localization and cell-to-cell interaction by spheroid modeling. RESULTS Three CTNND1 germline variants [c.28_29delinsCT, p.(Ala10Leu); c.1105C > T, p.(Pro369Ser); c.1537A > G, p.(Asn513Asp)] were identified in our EOGC cohorts. Cells encoding CTNND1 variants displayed altered E-cadherin levels and intercellular interactions. In addition, the p.(Pro369Ser) variant, located in a key region in the E-cadherin/p120ctn binding domain, showed E-cadherin mislocalization. CONCLUSIONS Defects in CTNND1 could be involved in germline predisposition to gastric cancer by altering E-cadherin and, consequently, cell-to-cell interactions. In the present study, CTNND1 germline variants explained 2% (3/172) of the cases, although further studies in larger external cohorts are needed.
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Affiliation(s)
- Cristina Herrera-Pariente
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Laia Bonjoch
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | | | - Yasmin Soares de Lima
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Romesa Mahmood
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology, Hospital Clínic, FRCB-IDIBAPS, CIBEREHD, 08036, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | | | - Gemma Llargués-Sistac
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Xavier Domínguez-Rovira
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Joan Llach
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Irina Luzko
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, UC San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, 08908, Barcelona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, 08908, Barcelona, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGI, 17190, Girona, Spain
| | | | - María Asunción García-González
- Instituto de Investigación Sanitaria Aragón, Instituto Aragonés de Ciencias de La Salud, CIBEREHD, 50009, Zaragoza, Spain
| | - Angel Lanas
- Instituto de Investigación Sanitaria Aragón, Instituto Aragonés de Ciencias de La Salud, CIBEREHD, 50009, Zaragoza, Spain
- Gastroenterology, Hospital Clínico Universitario de Zaragoza, Instituto de Investigación Sanitaria Aragón, Universidad de Zaragoza, CIBEREHD, 50009, Zaragoza, Spain
| | - Marta Carrillo
- Gastroenterology, Centro de Investigación Biomédica de Canarias (CIBICAN), Hospital Universitario de Canarias, Instituto Universitario de Tecnologías Biomédicas (ITB), Universidad de La Laguna, 38320, Santa Cruz de Tenerife, Spain
| | | | - Enrique Quintero
- Gastroenterology, Centro de Investigación Biomédica de Canarias (CIBICAN), Hospital Universitario de Canarias, Instituto Universitario de Tecnologías Biomédicas (ITB), Universidad de La Laguna, 38320, Santa Cruz de Tenerife, Spain
| | - Nuria Sala
- Unit of Nutrition and Cancer, Translational Research Laboratory, Catalan Institute of Oncology (ICO) and Bellvitge Biomedical Research Institute (IDIBELL), 08908, Barcelona, Spain
| | - Gemma Llort
- Medical Oncology, Parc Taulí University Hospital, 08208, Sabadell, Spain
| | - Lara Aguilera
- Gastroenterology, Vall d'Hebron Research Institute, 08035, Barcelona, Spain
| | - Laura Carot
- Gastroenterology, Hospital del Mar, 08003, Barcelona, Spain
| | | | - Rodrigo Jover
- Gastroenterology, Departamento de Medicina Clínica, Hospital General Universitario Dr. Balmis, Instituto de Investigación Sanitaria ISABIAL, Universidad Miguel Hernández, 03010, Alicante, Spain
| | | | - Joaquín Cubiella
- Gastroenterology, Complexo Hospitalario de Ourense, CIBEREHD, 32005, Ourense, Spain
| | - Antoni Castells
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Luis Bujanda
- Department of Hepatology and Gastroenterology, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Biodonostia Health Research Institute - Donostia University Hospital, Universidad del País Vasco (UPV/EHU), 20014, San Sebastián, Spain
| | - Sergi Castellví-Bel
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology, Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi I Sunyer (FRCB-IDIBAPS), CIBEREHD, Universitat de Barcelona, Hospital Clínic, Villarroel 170, 08036, Barcelona, Spain.
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain.
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Sultana T, Mou SI, Chatterjee D, Faruk MO, Hosen MI. Computational exploration of SLC14A1 genetic variants through structure modeling, protein-ligand docking, and molecular dynamics simulation. Biochem Biophys Rep 2024; 38:101703. [PMID: 38596408 PMCID: PMC11001776 DOI: 10.1016/j.bbrep.2024.101703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
The urea transporter UT-B1, encoded by the SLC14A1 gene, has been hypothesized to be a significant protein whose deficiency and dysfunction contribute to the pathogenesis of bladder cancer and many other diseases. Several studies reported the association of genetic alterations in the SLC14A1 (UT-B1) gene with bladder carcinogenesis, suggesting a need for thorough characterization of the UT-B1 protein's coding and non-coding variants. This study used various computational techniques to investigate the commonly occurring germ-line missense and non-coding SNPs (ncSNPs) of the SLC14A1 gene (UT-B1) for their structural, functional, and molecular implications for disease susceptibility and dysfunctionality. SLC14A1 missense variants, primarily identified from the ENSEMBL genome browser, were screened through twelve functionality prediction tools leading to two variants D280Y (predicted detrimental by maximum tools) and D280N (high global MAF) for rs1058396. Subsequently, the ConSurf and NetSurf tools revealed the D280 residue to be in a variable site and exposed on the protein surface. According to I-Mutant2.0 and MUpro, both variants are predicted to cause a significant effect on protein stability. Analysis of molecular docking anticipated these two variants to decrease the binding affinity of UT-B1 protein for the examined ligands to a significant extent. Molecular dynamics also disclosed the possible destabilization of the UT-B1 protein due to single nucleotide polymorphism compared to wild-type protein which may result in impaired protein function. Furthermore, several non-coding SNPs were estimated to affect transcription factor binding and regulation of SLC14A1 gene expression. Additionally, two ncSNPs were found to affect miRNA-based post-transcriptional regulation by creating new seed regions for miRNA binding. This comprehensive in-silico study of SLC14A1 gene variants may serve as a springboard for future large-scale investigations examining SLC14A1 polymorphisms.
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Affiliation(s)
- Tamanna Sultana
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Sadia Islam Mou
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md. Omar Faruk
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
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Stefanova E, Marjanović A, Dobričić V, Mandić-Stojmenović G, Stojković T, Branković M, Šarčević M, Novaković I, Kostić VS. Frequency of C9orf72, GRN, and MAPT pathogenic variants in patients recruited at the Belgrade Memory Center. Neurogenetics 2024; 25:193-200. [PMID: 38847891 DOI: 10.1007/s10048-024-00766-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/02/2024] [Indexed: 07/16/2024]
Abstract
Most of the heritability in frontotemporal dementia (FTD) is accounted for by autosomal dominant hexanucleotide expansion in the chromosome 9 open reading frame 72 (C9orf72), pathogenic/likely pathogenic variants in progranulin (GRN), and microtubule-associated protein tau (MAPT) genes. Until now, there has been no systematic analysis of these genes in the Serbian population. Herein, we assessed the frequency of the C9orf72 expansion, pathogenic/likely pathogenic variants in GRN and MAPT in a well-characterized group of 472 subjects (FTD, Alzheimer's disease - AD, mild cognitive impairment - MCI, and unspecified dementia - UnD), recruited in the Memory Center, Neurology Clinic, University Clinical Center of Serbia. The C9orf72 repeat expansion was detected in 6.98% of FTD cases (13.46% familial; 2.6% sporadic). In the UnD subgroup, C9orf72 repeat expansions were detected in 4.08% (8% familial) individuals. Pathogenic variants in the GRN were found in 2.85% of familial FTD cases. Interestingly, no MAPT pathogenic/likely pathogenic variants were detected, suggesting possible geographical specificity. Our findings highlight the importance of wider implementation of genetic testing in neurological and psychiatric practice managing patients with cognitive-behavioral and motor symptoms.
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Affiliation(s)
- Elka Stefanova
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia.
- Neurology Clinic, University Clinical Center of Serbia (UCCS), Dr Subotića 6, Belgrade, 11000, Serbia.
| | - Ana Marjanović
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia
| | - Valerija Dobričić
- Neurology Clinic, University Clinical Center of Serbia (UCCS), Dr Subotića 6, Belgrade, 11000, Serbia
- University of Lübeck-Lübeck Interdisciplinary Platform for Genome Analytics, 11000, Lübeck, Germany
| | - Gorana Mandić-Stojmenović
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia
- Neurology Clinic, University Clinical Center of Serbia (UCCS), Dr Subotića 6, Belgrade, 11000, Serbia
| | - Tanja Stojković
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia
- Neurology Clinic, University Clinical Center of Serbia (UCCS), Dr Subotića 6, Belgrade, 11000, Serbia
| | - Marija Branković
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia
| | - Maksim Šarčević
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia
| | - Ivana Novaković
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia
- Neurology Clinic, University Clinical Center of Serbia (UCCS), Dr Subotića 6, Belgrade, 11000, Serbia
| | - Vladimir S Kostić
- Faculty of Medicine, University of Belgrade, Dr Subotića 8, Belgrade, 11000, Serbia
- Neurology Clinic, University Clinical Center of Serbia (UCCS), Dr Subotića 6, Belgrade, 11000, Serbia
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Kamal MM, Teeya ST, Rahman MM, Talukder MEK, Sarmin S, Wani TA, Hasan MM. Prediction and assessment of deleterious and disease causing nonsynonymous single nucleotide polymorphisms (nsSNPs) in human FOXP4 gene: An in - silico study. Heliyon 2024; 10:e32791. [PMID: 38994097 PMCID: PMC11237951 DOI: 10.1016/j.heliyon.2024.e32791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/10/2024] [Indexed: 07/13/2024] Open
Abstract
In humans, FOXP gene family is involved in embryonic development and cancer progression. The FOXP4 (Forkhead box protein P4) gene belongs to this FOXP gene family. FOXP4 gene plays a crucial role in oncogenesis. Single nucleotide polymorphisms are biological markers and common determinants of human diseases. Mutations can largely affect the function of the corresponding protein. Therefore, the molecular mechanism of nsSNPs in the FOXP4 gene needs to be elucidated. Initially, the SNPs of the FOXP4 gene were extracted from the dbSNP database and a total of 23124 SNPs was found, where 555 nonsynonymous, 20525 intronic, 1114 noncoding transcript, 334 synonymous were obtained and the rest were unspecified. Then, a series of bioinformatics tools (SIFT, PolyPhen2, SNAP2, PhD SNP, PANTHER, I-Mutant2.0, MUpro, GOR IV, ConSurf, NetSurfP 2.0, HOPE, DynaMut2, GeneMANIA, STRING and Schrodinger) were used to explore the effect of nsSNPs on FOXP4 protein function and structural stability. First, 555 nsSNPs were analyzed using SIFT, of which 57 were found as deleterious. Following, PolyPhen2, SNAP2, PhD SNP and PANTHER analyses, 10 nsSNPs (rs372762294, rs141899153, rs142575732, rs376938850, rs367607523, rs112517943, rs140387832, rs373949416, rs373949416 and rs376160648) were common and observed as deleterious, damaging and diseases associated. Following that, using I-Mutant2.0 and MUpro servers, 7 nsSNPs were found to be the most unstable. GOR IV predicted that these seven nsSNPs affect protein structure by altering the protein contents of alpha helixes, extended strands, and random coils. Following DynaMut2, 5 nsSNPs showed a decrease in the ΔΔG value compared with the wild-type and were found to be responsible for destabilizing the corresponding protein. GeneMANIA and STRING network revealed interaction of FOXP4 with other genes. Finally, molecular dynamics simulation analysis revealed consistent fluctuation in RMSD and RMSF values, Rg and hydrogen bonds in the mutant proteins compared with WT, which might alter the functional and structural stability of the corresponding protein. As a result, the aforementioned integrated comprehensive bioinformatic analyses provide insight into how various nsSNPs of the FOXP4 gene change the structural and functional properties of the corresponding protein, potentially proceeding with the pathophysiology of human diseases.
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Affiliation(s)
- Md Mostafa Kamal
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre, Jashore, 7408, Bangladesh
| | - Shamiha Tabassum Teeya
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Mahfuzur Rahman
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, 1216, Bangladesh
| | - Md Enamul Kabir Talukder
- Department of Genetic Engineering & Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre, Jashore, 7408, Bangladesh
| | - Sonia Sarmin
- BIRTAN-Bangladesh Institute of Research and Training on Applied Nutrition, Jhenaidah, 7300, Bangladesh
| | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
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Lin YJ, Menon AS, Hu Z, Brenner SE. Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600283. [PMID: 38979289 PMCID: PMC11230257 DOI: 10.1101/2024.06.25.600283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background Variant interpretation is essential for identifying patients' disease-causing genetic variants amongst the millions detected in their genomes. Hundreds of Variant Impact Predictors (VIPs), also known as Variant Effect Predictors (VEPs), have been developed for this purpose, with a variety of methodologies and goals. To facilitate the exploration of available VIP options, we have created the Variant Impact Predictor database (VIPdb). Results The Variant Impact Predictor database (VIPdb) version 2 presents a collection of VIPs developed over the past 25 years, summarizing their characteristics, ClinGen calibrated scores, CAGI assessment results, publication details, access information, and citation patterns. We previously summarized 217 VIPs and their features in VIPdb in 2019. Building upon this foundation, we identified and categorized an additional 186 VIPs, resulting in a total of 403 VIPs in VIPdb version 2. The majority of the VIPs have the capacity to predict the impacts of single nucleotide variants and nonsynonymous variants. More VIPs tailored to predict the impacts of insertions and deletions have been developed since the 2010s. In contrast, relatively few VIPs are dedicated to the prediction of splicing, structural, synonymous, and regulatory variants. The increasing rate of citations to VIPs reflects the ongoing growth in their use, and the evolving trends in citations reveal development in the field and individual methods. Conclusions VIPdb version 2 summarizes 403 VIPs and their features, potentially facilitating VIP exploration for various variant interpretation applications. Availability VIPdb version 2 is available at https://genomeinterpretation.org/vipdb.
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Affiliation(s)
- Yu-Jen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
| | - Arul S. Menon
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, California 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Currently at: Illumina, Foster City, California 94404, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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19
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Legarrea JMA, Alves HDS, Chaves RRM, Soares CD, Robinson L, van Heerden WFP, de Andrade BAB, Polti LF, de Souza SF, Gomez RS, de Cáceres CVBL, Vargas PA, Fonseca FP. Histiocytic sarcoma affecting the oral cavity: a clinical, pathologic and molecular study. Oral Surg Oral Med Oral Pathol Oral Radiol 2024:S2212-4403(24)00368-7. [PMID: 39048487 DOI: 10.1016/j.oooo.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
OBJECTIVE To investigate the clinicopathological, immunohistochemical and molecular features of histiocytic sarcomas affecting the oral cavity. METHODS Pathology files of two institutions were searched for cases of histiocytic sarcoma, and new H&E-stained slides and immunohistochemistry reactions evaluated for diagnosis confirmation. Molecular screening for KRAS and PIK3CA mutations was performed through polymerase chain reaction (PCR) followed by Sanger sequencing. BRAFp.V600E mutation was assessed by pyrosequencing. Clinical data regarding sex, age, tumor location, systemic manifestations, clinical presentation, follow-up time, treatment applied and status at last follow-up were collected from patients' pathology and medical files. RESULTS Three cases were retrieved during the period investigated (2000-2023). Two females and one male were affected, with a wide age range, involving the tongue, palate and gingiva. Histopathologically, the neoplasms presented as highly pleomorphic atypical cells distributed diffusely with infiltration of normal structures. All cases demonstrated histiocytic differentiation expressing CD68 and CD163, and a high Ki67 expression. Genetic mutations were evaluated in two cases. One case harboured BRAF-V600E mutation, but not in KRAS and PIK3CA, while the second case did not show mutation in BRAF-V600E, KRAS and PI3KCA. One patient was lost, and two patients died after eight and four months of follow-up. CONCLUSION Histiocytic sarcomas involving the oral cavity are extremely rare, and may represent dissemination of a systemic condition. It has an aggressive biological behaviour with a poor overall prognosis.
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Affiliation(s)
- Juan Manuel Arteaga Legarrea
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Humberto de Souza Alves
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Roberta Rayra Martins Chaves
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Liam Robinson
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Willie F P van Heerden
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; PathCare Vermaak Histopathology, Centurion, Pretoria, South Africa
| | | | - Lucas Fabian Polti
- Pathology, School of Dentistry, University of Buenos Aires, Buenos Aires, Argentina
| | - Silvia Ferreira de Souza
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Pablo Agustin Vargas
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
| | - Felipe Paiva Fonseca
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
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20
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Vuong LT, Mlodzik M. Wg/Wnt-signaling-induced nuclear translocation of β-catenin is attenuated by a β-catenin peptide through its interference with the IFT-A complex. Cell Rep 2024; 43:114362. [PMID: 38870008 DOI: 10.1016/j.celrep.2024.114362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 04/09/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Wnt/Wingless (Wg) signaling is critical in development and disease, including cancer. Canonical Wnt signaling is mediated by β-catenin/Armadillo (Arm in Drosophila) transducing signals to the nucleus, with IFT-A/Kinesin 2 complexes promoting nuclear translocation of β-catenin/Arm. Here, we demonstrate that a conserved small N-terminal Arm34-87/β-catenin peptide binds to IFT140, acting as a dominant interference tool to attenuate Wg/Wnt signaling in vivo. Arm34-87 expression antagonizes endogenous Wnt/Wg signaling, resulting in the reduction of its target expression. Arm34-87 inhibits Wg/Wnt signaling by interfering with nuclear translocation of endogenous Arm/β-catenin, and this can be modulated by levels of wild-type β-catenin or IFT140, with the Arm34-87 effect being enhanced or suppressed. Importantly, this mechanism is conserved in mammals with the equivalent β-catenin24-79 peptide blocking nuclear translocation and pathway activation, including in cancer cells. Our work indicates that Wnt signaling can be regulated by a defined N-terminal β-catenin peptide and thus might serve as an entry point for therapeutic applications to attenuate Wnt/β-catenin signaling.
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Affiliation(s)
- Linh T Vuong
- Department of Cell, Developmental, and Regenerative Biology, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
| | - Marek Mlodzik
- Department of Cell, Developmental, and Regenerative Biology, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA.
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21
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Rosenberg FM, van der Most PJ, Loman L, Kamali Z, Dittmar D, Snieder H, Schuttelaar MLA. A genome-wide association study of hand eczema identifies locus 20q13.33 and reveals genetic overlap with atopic dermatitis. Contact Dermatitis 2024. [PMID: 38924601 DOI: 10.1111/cod.14619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Twin studies revealed that genetic effects play a role in hand eczema (HE), but the responsible genetic factors are unknown. OBJECTIVES To identify and characterise genetic loci associated with HE and to provide insight into the genetic overlap between HE and atopic dermatitis (AD). METHODS We used questionnaire-derived and genotype data from the European population-based Lifelines cohort and biobank. We performed a discovery genome-wide association study (GWAS) of HE (2879 cases and 16 249 controls) and of AD (1706 cases and 17 190 controls). We replicated our findings in an independent Lifelines sample for HE (1188 cases and 6431 controls) and AD (757 cases and 6747 controls). We conducted several post-GWAS analyses and performed genetic correlation analyses between our HE results and independent AD data. RESULTS The two-step GWAS of HE, regardless of adjusting for AD, identified one independent locus 20q13.33, likely driven by a number of causal single-nucleotide polymorphisms. For the AD GWAS, we replicated a known stop-gained rs61816761 at locus 1q21.3 (FLG, FLGAS1). We found a strong genetic correlation (p < 0.01) between HE and AD (rg = 0.65), regardless of adjusting for AD (rg = 0.63). CONCLUSIONS Locus 20q13.33 is associated with HE, and there is a large genetic overlap between HE and AD.
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Affiliation(s)
- Fieke M Rosenberg
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Peter J van der Most
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Laura Loman
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zoha Kamali
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Bioinformatics, School of Advanced Medical Technologies, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Daan Dittmar
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marie L A Schuttelaar
- Department of Dermatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Richards T, Wilson P, Goggolidou P. Next generation sequencing identifies WNT signalling as a significant pathway in Autosomal Recessive Polycystic Kidney Disease (ARPKD) manifestation and may be linked to disease severity. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167309. [PMID: 38885798 DOI: 10.1016/j.bbadis.2024.167309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
INTRODUCTION Autosomal Recessive Polycystic Kidney Disease (ARPKD) is a rare paediatric disease primarily caused by sequence variants in PKHD1. ARPKD presents with considerable clinical variability relating to the type of PKHD1 sequence variant, but not its position. Animal models of Polycystic Kidney Disease (PKD) suggest a complex genetic landscape, with genetic modifiers as a potential cause of disease variability. METHODS To investigate in an unbiased manner the molecular mechanisms of ARPKD and identify potential indicators of disease severity, Whole Exome Sequencing (WES) and RNA-Sequencing (RNA-Seq) were employed on human ARPKD kidneys and age-matched healthy controls. RESULTS WES confirmed the clinical diagnosis of ARPKD in our patient cohort consisting of ten ARPKD kidneys. Sequence variant type, nor position of PKHD1 sequence variants, was linked to disease severity. Sequence variants in genes associated with other ciliopathies were detected in the ARPKD cohort, but only PKD1 could be linked to disease severity. Transcriptomic analysis on a subset of four ARPKD kidneys representing severe and moderate ARPKD, identified a significant number of genes relating to WNT signalling, cellular metabolism and development. Increased expression of WNT signalling-related genes was validated by RT-qPCR in severe and moderate ARPKD kidneys. Two individuals in our cohort with the same PKHD1 sequence variants but different rates of kidney disease progression, with displayed transcriptomic differences in the expression of WNT signalling genes. CONCLUSION ARPKD kidney transcriptomics highlights changes in WNT signalling as potentially significant in ARPKD manifestation and severity, providing indicators for slowing down the progression of ARPKD.
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Affiliation(s)
- Taylor Richards
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Patricia Wilson
- Centre for Nephrology, UCL Medical School, Royal Free Campus, Rowland Hill, London NW3 2PF, UK
| | - Paraskevi Goggolidou
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK.
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Navapour L, Mogharrab N, Parvin A, Rezaei Arablouydareh S, Movahedpour A, Jebraeily M, Taheri-Anganeh M, Ghasemnejad-Berenji H. Identification of high-risk non-synonymous SNPs (nsSNPs) in DNAH1 and DNAH17 genes associated with male infertility: a bioinformatics analysis. J Appl Genet 2024:10.1007/s13353-024-00884-x. [PMID: 38874855 DOI: 10.1007/s13353-024-00884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
Male infertility is a significant reproductive issue affecting a considerable number of couples worldwide. While there are various causes of male infertility, genetic factors play a crucial role in its development. We focused on identifying and analyzing the high-risk nsSNPs in DNAH1 and DNAH17 genes, which encode proteins involved in sperm motility. A total of 20 nsSNPs for DNAH1 and 10 nsSNPs for DNAH17 were analyzed using various bioinformatics tools including SIFT, PolyPhen-2, CADD, PhD-SNPg, VEST-4, and MutPred2. As a result, V1287G, L2071R, R2356W, R3169C, R3229C, E3284K, R4096L, R4133C, and A4174T in DNAH1 gene and C1803Y, C1829Y, R1903C, and L3595P in DNAH17 gene were identified as high-risk nsSNPs. These nsSNPs were predicted to decrease protein stability, and almost all were found in highly conserved amino acid positions. Additionally, 4 nsSNPs were observed to alter post-translational modification status. Furthermore, the interaction network analysis revealed that DNAH1 and DNAH17 interact with DNAH2, DNAH3, DNAH5, DNAH7, DNAH8, DNAI2, DNAL1, CFAP70, DNAI3, DNAI4, ODAD1, and DNAI7, demonstrating the importance of DNAH1 and DNAH17 proteins in the overall functioning of the sperm motility machinery. Taken together, these findings revealed the detrimental effects of identified high-risk nsSNPs on protein structure and function and highlighted their potential relevance to male infertility. Further studies are warranted to validate these findings and to elucidate the underlying mechanisms.
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Affiliation(s)
- Leila Navapour
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Navid Mogharrab
- Biophysics and Computational Biology Laboratory (BCBL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Ali Parvin
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Sahar Rezaei Arablouydareh
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohamad Jebraeily
- Department of Health Information Technology, School of Allied Medical Sciences, Urmia University of Medical Sciences, Urmia, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran.
| | - Hojat Ghasemnejad-Berenji
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran.
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Maggi J, Koller S, Feil S, Bachmann-Gagescu R, Gerth-Kahlert C, Berger W. Limited Added Diagnostic Value of Whole Genome Sequencing in Genetic Testing of Inherited Retinal Diseases in a Swiss Patient Cohort. Int J Mol Sci 2024; 25:6540. [PMID: 38928247 PMCID: PMC11203445 DOI: 10.3390/ijms25126540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The purpose of this study was to assess the added diagnostic value of whole genome sequencing (WGS) for patients with inherited retinal diseases (IRDs) who remained undiagnosed after whole exome sequencing (WES). WGS was performed for index patients in 66 families. The datasets were analyzed according to GATK's guidelines. Additionally, DeepVariant was complemented by GATK's workflow, and a novel structural variant pipeline was developed. Overall, a molecular diagnosis was established in 19/66 (28.8%) index patients. Pathogenic deletions and one deep-intronic variant contributed to the diagnostic yield in 4/19 and 1/19 index patients, respectively. The remaining diagnoses (14/19) were attributed to exonic variants that were missed during WES analysis due to bioinformatic limitations, newly described loci, or unclear pathogenicity. The added diagnostic value of WGS equals 5/66 (9.6%) for our cohort, which is comparable to previous studies. This figure would decrease further to 1/66 (1.5%) with a standardized and reliable copy number variant workflow during WES analysis. Given the higher costs and limited added value, the implementation of WGS as a first-tier assay for inherited eye disorders in a diagnostic laboratory remains untimely. Instead, progress in bioinformatic tools and communication between diagnostic and clinical teams have the potential to ameliorate diagnostic yields.
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Affiliation(s)
- Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
| | | | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland;
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (S.F.)
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
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25
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Ko YL, Tuan WL, Teng MS, Su WC, Wang CC, Er LK, Wu S, Hsu LA. SLC10A1 rs2296651 variant (S267F mutation) predicts biochemical traits, hepatitis B virus infection susceptibility and the risk of gallstone disease. Mol Genet Genomics 2024; 299:62. [PMID: 38869622 DOI: 10.1007/s00438-024-02153-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Sodium taurocholate co-transporting polypeptide (NTCP), a bile acid transporter, plays a crucial role in regulating bile acid levels and influencing the risk of HBV infection. Genetic variations in the SLC10A1 gene, which encodes NTCP, affect these functions. However, the impact of SLC10A1 gene variants on the metabolic and biochemical traits remained unclear. We aimed to investigate the association of SLC10A1 gene variants with the clinical and biochemical parameters, and the risk of different HBV infection statuses and gallstone disease in the Taiwanese population. Genotyping data from 117,679 Taiwan Biobank participants were analyzed using the Axiom genome-wide CHB arrays. Regional-plot association analysis demonstrated genome-wide significant association between the SLC10A1 rs2296651 genotypes and lipid profile, gamma glutamyl transferase (γGT) level and anti-HBc-positivity. Genotype-phenotype association analyses revealed significantly lower total cholesterol, low-density lipoprotein (LDL) cholesterol and uric acid levels, a higher γGT level and a higher gallstone incidence in rare rs2296651-A allele carrier. Participants with the rs2296651 AA-genotype exhibited significantly lower rates of anti-HBc-positivity and HBsAg-positivity. Compared to those with the GG-genotype, individuals with non-GG-genotypes had reduced risks for various HBV infection statuses: the AA-genotype showed substantially lower risks, while the GA-genotype demonstrated modestly lower risks. Predictive tools also suggested that the rs2296651 variant potentially induced protein damage and pathogenic effects. In conclusion, our data revealed pleiotropic effects of the SLC10A1 rs2296651 genotypes on the levels of biochemical traits and the risk of HBV infection and gallstone disease. This confirms SLC10A1's versatility and implicates its genotypes in predicting both biochemical traits and disease susceptibility.
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Affiliation(s)
- Yu-Lin Ko
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei city, Taiwan.
- Department of Research, Division of Cardiology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, No.289, Jianguo Road., Xindian Dist, New Taipei City, 23142, Taiwan.
- School of Medicine, Tzu Chi University, Hualien, Taiwan.
| | - Wei-Lun Tuan
- Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Ming-Sheng Teng
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei city, Taiwan
| | - Wei-Chih Su
- School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Gastroenterology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei city, Taiwan
| | - Chia-Chi Wang
- School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Gastroenterology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei city, Taiwan
| | - Leay-Kiaw Er
- School of Medicine, Tzu Chi University, Hualien, Taiwan
- The Division of Endocrinology and Metabolism, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, 23142, Taiwan
| | - Semon Wu
- Department of Life Science, Chinese Culture University, Taipei, Taiwan
| | - Lung-An Hsu
- The First Cardiovascular Division, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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26
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Shajan B, Marri S, Bastiampillai T, Gregory KJ, Hellyer SD, Nair PC. Trace amine associated receptor 1: predicted effects of single nucleotide variants on structure-function in geographically diverse populations. Hum Genomics 2024; 18:61. [PMID: 38863077 PMCID: PMC11165750 DOI: 10.1186/s40246-024-00620-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Trace Amine Associated Receptor 1 (TAAR1) is a novel pharmaceutical target under investigation for the treatment of several neuropsychiatric conditions. TAAR1 single nucleotide variants (SNV) have been found in patients with schizophrenia and metabolic disorders. However, the frequency of variants in geographically diverse populations and the functional effects of such variants are unknown. In this study, we aimed to characterise the distribution of TAAR1 SNVs in five different WHO regions using the Database of Genotypes and Phenotypes (dbGaP) and conducted a critical computational analysis using available TAAR1 structural data to identify SNVs affecting ligand binding and/or functional regions. Our analysis shows 19 orthosteric, 9 signalling and 16 micro-switch SNVs hypothesised to critically influence the agonist induced TAAR1 activation. These SNVs may non-proportionally influence populations from discrete regions and differentially influence the activity of TAAR1-targeting therapeutics in genetically and geographically diverse populations. Notably, our dataset presented with orthosteric SNVs D1033.32N (found only in the South-East Asian Region and Western Pacific Region) and T1945.42A (found only in South-East Asian Region), and 2 signalling SNVs (V1253.54A/T2526.36A, found in African Region and commonly, respectively), all of which have previously demonstrated to influence ligand induced functions of TAAR1. Furthermore, bioinformatics analysis using SIFT4G, MutationTaster 2, PROVEAN and MutationAssessor predicted all 16 micro-switch SNVs are damaging and may further influence the agonist activation of TAAR1, thereby possibly impacting upon clinical outcomes. Understanding the genetic basis of TAAR1 function and the impact of common mutations within clinical populations is important for the safe and effective utilisation of novel and existing pharmacotherapies.
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Affiliation(s)
- Britto Shajan
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Shashikanth Marri
- Flinders Health and Medical Research Institute (FHMRI) College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tarun Bastiampillai
- Department of Psychiatry, Monash University, Parkville, Melbourne, VIC, Australia
- Discipline of Psychiatry, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Karen J Gregory
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Melbourne, VIC, 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Shane D Hellyer
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Melbourne, VIC, 3052, Australia
| | - Pramod C Nair
- Discipline of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
- Flinders Health and Medical Research Institute (FHMRI) College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
- South Australian Health and Medical Research Institute, University of Adelaide, Adelaide, South Australia, Australia.
- Discipline of Medicine, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.
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27
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Abuzaid O, Idris AB, Yılmaz S, Idris EB, Idris LB, Hassan MA. Prediction of the most deleterious non-synonymous SNPs in the human IL1B gene: evidence from bioinformatics analyses. BMC Genom Data 2024; 25:56. [PMID: 38858637 PMCID: PMC11163699 DOI: 10.1186/s12863-024-01233-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Polymorphisms in IL1B play a significant role in depression, multiple inflammatory-associated disorders, and susceptibility to infection. Functional non-synonymous SNPs (nsSNPs) result in changes in the encoded amino acids, potentially leading to structural and functional alterations in the mutant proteins. So far, most genetic studies have concentrated on SNPs located in the IL1B promoter region, without addressing nsSNPs and their association with multifactorial diseases. Therefore, this study aimed to explore the impact of deleterious nsSNPs retrieved from the dbSNP database on the structure and functions of the IL1B protein. RESULTS Six web servers (SIFT, PolyPhen-2, PROVEAN, SNPs&GO, PHD-SNP, PANTHER) were used to analyze the impact of 222 missense SNPs on the function and structure of IL1B protein. Five novel nsSNPs (E100K, T240I, S53Y, D128Y, and F228S) were found to be deleterious and had a mutational impact on the structure and function of the IL1B protein. The I-mutant v2.0 and MUPro servers predicted that these mutations decreased the stability of the IL1B protein. Additionally, these five mutations were found to be conserved, underscoring their significance in protein structure and function. Three of them (T240I, D128Y, and F228S) were predicted to be cancer-causing nsSNPs. To analyze the behavior of the mutant structures under physiological conditions, we conducted a 50 ns molecular dynamics simulation using the WebGro online tool. Our findings indicate that the mutant values differ from those of the IL1B wild type in terms of RMSD, RMSF, Rg, SASA, and the number of hydrogen bonds. CONCLUSIONS This study provides valuable insights into nsSNPs located in the coding regions of IL1B, which lead to direct deleterious effects on the functional and structural aspects of the IL1B protein. Thus, these nsSNPs could be considered significant candidates in the pathogenesis of disorders caused by IL1B dysfunction, contributing to effective drug discovery and the development of precision medications. Thorough research and wet lab experiments are required to verify our findings. Moreover, bioinformatic tools were found valuable in the prediction of deleterious nsSNPs.
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Affiliation(s)
- Ola Abuzaid
- Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Abeer Babiker Idris
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan.
| | - Semih Yılmaz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
- Erciyes Teknopark, Promoseed Biotechnology A.Ş, Kayseri, Turkey
| | - Einass Babikir Idris
- Department of Medical Microbiology, Rashid Medical Complex, Riyadh, Saudi Arabia
| | | | - Mohamed A Hassan
- Department of Bioinformatics, Africa City of Technology, Khartoum, Sudan
- Sanimed International Lab and Management L.L.C, Abu Dhabi, UAE
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28
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Yang F, Begemann A, Reichhart N, Haeckel A, Steindl K, Schellenberger E, Sturm RF, Barth M, Bassani S, Boonsawat P, Courtin T, Delobel B, Gunning B, Hardies K, Jennesson M, Legoff L, Linnankivi T, Prouteau C, Smal N, Spodenkiewicz M, Toelle SP, Van Gassen K, Van Paesschen W, Verbeek N, Ziegler A, Zweier M, Horn AHC, Sticht H, Lerche H, Weckhuysen S, Strauß O, Rauch A. Missense variants in ANO4 cause sporadic encephalopathic or familial epilepsy with evidence for a dominant-negative effect. Am J Hum Genet 2024; 111:1184-1205. [PMID: 38744284 PMCID: PMC11179416 DOI: 10.1016/j.ajhg.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
Anoctamins are a family of Ca2+-activated proteins that may act as ion channels and/or phospholipid scramblases with limited understanding of function and disease association. Here, we identified five de novo and two inherited missense variants in ANO4 (alias TMEM16D) as a cause of fever-sensitive developmental and epileptic or epileptic encephalopathy (DEE/EE) and generalized epilepsy with febrile seizures plus (GEFS+) or temporal lobe epilepsy. In silico modeling of the ANO4 structure predicted that all identified variants lead to destabilization of the ANO4 structure. Four variants are localized close to the Ca2+ binding sites of ANO4, suggesting impaired protein function. Variant mapping to the protein topology suggests a preliminary genotype-phenotype correlation. Moreover, the observation of a heterozygous ANO4 deletion in a healthy individual suggests a dysfunctional protein as disease mechanism rather than haploinsufficiency. To test this hypothesis, we examined mutant ANO4 functional properties in a heterologous expression system by patch-clamp recordings, immunocytochemistry, and surface expression of annexin A5 as a measure of phosphatidylserine scramblase activity. All ANO4 variants showed severe loss of ion channel function and DEE/EE associated variants presented mild loss of surface expression due to impaired plasma membrane trafficking. Increased levels of Ca2+-independent annexin A5 at the cell surface suggested an increased apoptosis rate in DEE-mutant expressing cells, but no changes in Ca2+-dependent scramblase activity were observed. Co-transfection with ANO4 wild-type suggested a dominant-negative effect. In summary, we expand the genetic base for both encephalopathic sporadic and inherited fever-sensitive epilepsies and link germline variants in ANO4 to a hereditary disease.
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Affiliation(s)
- Fang Yang
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Anais Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Nadine Reichhart
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Akvile Haeckel
- Institute for Radiology and Children's Radiology, Charité-Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Eyk Schellenberger
- Institute for Radiology and Children's Radiology, Charité-Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Ronja Fini Sturm
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Magalie Barth
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Sissy Bassani
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Paranchai Boonsawat
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Thomas Courtin
- Sorbonne Université, INSERM, CNRS, Institut du Cerveau - Paris Brain Institute - ICM, 75013 Paris, France; Hôpital Pitié-Salpêtrière, DMU BioGe'M, AP-HP, 75013 Paris, France
| | - Bruno Delobel
- Service de Cytogénétique, GH de l'Institut Catholique de Lille, Hopital Saint Vincent de Paul, Lille, France
| | | | - Katia Hardies
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Louis Legoff
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Tarja Linnankivi
- Epilepsia Helsinki, University of Helsinki and Helsinki University Hospital, 00029 HUS Helsinki, Finland; Department of Pediatric Neurology and Pediatric Research Center, New Children's Hospital, Helsinki University Hospital and University of Helsinki, 00029 HUS Helsinki, Finland
| | - Clément Prouteau
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Noor Smal
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerp, Belgium
| | - Marta Spodenkiewicz
- Department of Genetics, La Réunion University Hospital, Saint-Pierre, France
| | - Sandra P Toelle
- Department of Pediatric Neurology, Children's University Hospital Zurich, Zurich, Switzerland
| | - Koen Van Gassen
- University Medical Center Utrecht, Department of Genetics, Utrecht, the Netherlands
| | - Wim Van Paesschen
- Laboratory for Epilepsy Research, KU Leuven, and Neurology Department, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Nienke Verbeek
- University Medical Center Utrecht, Department of Genetics, Utrecht, the Netherlands
| | - Alban Ziegler
- University Hospital of Angers, Department of Genetics, Angers, France
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Sarah Weckhuysen
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, University of Antwerp, 2610 Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium; Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, 2610 Antwerp, Belgium
| | - Olaf Strauß
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität, Humboldt-University, the Berlin Institute of Health, Berlin, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; Children's University Hospital Zurich, Zurich, Switzerland.
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29
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Takeda Y, Ueki M, Matsuhiro J, Walinda E, Tanaka T, Yamada M, Fujita H, Takezaki S, Kobayashi I, Tamaki S, Nagata S, Miyake N, Matsumoto N, Osawa M, Yasumi T, Heike T, Ohtake F, Saito MK, Toguchida J, Takita J, Ariga T, Iwai K. A de novo dominant-negative variant is associated with OTULIN-related autoinflammatory syndrome. J Exp Med 2024; 221:e20231941. [PMID: 38652464 PMCID: PMC11040501 DOI: 10.1084/jem.20231941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
OTULIN-related autoinflammatory syndrome (ORAS), a severe autoinflammatory disease, is caused by biallelic pathogenic variants of OTULIN, a linear ubiquitin-specific deubiquitinating enzyme. Loss of OTULIN attenuates linear ubiquitination by inhibiting the linear ubiquitin chain assembly complex (LUBAC). Here, we report a patient who harbors two rare heterozygous variants of OTULIN (p.P152L and p.R306Q). We demonstrated accumulation of linear ubiquitin chains upon TNF stimulation and augmented TNF-induced cell death in mesenchymal stem cells differentiated from patient-derived iPS cells, which confirms that the patient has ORAS. However, although the de novo p.R306Q variant exhibits attenuated deubiquitination activity without reducing the amount of OTULIN, the deubiquitination activity of the p.P152L variant inherited from the mother was equivalent to that of the wild-type. Patient-derived MSCs in which the p.P152L variant was replaced with wild-type also exhibited augmented TNF-induced cell death and accumulation of linear chains. The finding that ORAS can be caused by a dominant-negative p.R306Q variant of OTULIN furthers our understanding of disease pathogenesis.
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Affiliation(s)
- Yukiko Takeda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Ueki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junpei Matsuhiro
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masafumi Yamada
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
- Department of Food and Human Wellness, Rakuno Gakuen University, Ebetsu, Japan
| | - Hiroaki Fujita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunichiro Takezaki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ichiro Kobayashi
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Sakura Tamaki
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sanae Nagata
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Megumu K. Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junya Toguchida
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Ariga
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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30
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Aggarwal S, Vineeth VS, Padwal SS, Bhat SA, Singh A, Kulkarni A, Patil M, Tallapaka K, Pasumarthi D, Venkatapuram V, Thotakura PL, Dalal A, Bhandari R. SERPINA11 related novel serpinopathy - A perinatal lethal disorder. Clin Genet 2024. [PMID: 38831697 DOI: 10.1111/cge.14564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
SERPINA11 is a hitherto poorly characterised gene belonging to Clade A of the SERPIN superfamily, with unknown expression pattern and functional significance. We report a perinatal lethal phenotype in two foetuses from the same family associated with a biallelic loss of function variant in SERPINA11, and provide functional evidence to support its candidature as a Mendelian disorder. The SERPINA11 variant-associated foetal phenotype is characterised by gross and histopathological features of extracellular matrix disruption. Western blot and immunofluorescence analyses revealed SERPINA11 expression in multiple mouse tissues, with pronounced expression in the bronchiolar epithelium. We observed a significant decrease in SERPINA11 immunofluorescence in the affected foetal lung compared with a healthy gestation-matched foetus. Protein expression data from HEK293T cell lines following site-directed mutagenesis support the loss of function nature of the variant. Transcriptome analysis from the affected foetal liver indicated the possibility of reduced SERPINA11 transcript abundance. This novel serpinopathy appears to be a consequence of the loss of inhibition of serine proteases involved in extracellular matrix remodelling, revealing SERPINA11 as a protease inhibitor critical for embryonic development.
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Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Venugopal Satidevi Vineeth
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shrutika S Padwal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Manipal Academy of Higher Education, Manipal, India
| | - Sameer Ahmed Bhat
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Arpita Singh
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Aditya Kulkarni
- Department of Histopathology, Apollo Hospitals, Hyderabad, India
| | - Mallikarjun Patil
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | | | - Divya Pasumarthi
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vijayasree Venkatapuram
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Pragna Lakshmi Thotakura
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Lopes EC, Shi F, Sawant A, Ibrahim M, Gomez-Jenkins M, Hu Z, Manchiraju P, Bhatt V, Wang W, Hinrichs CS, Wallace DC, Su X, Rabinowitz JD, Chan CS, Guo JY, Ganesan S, Lattime EC, White E. RESPIRATION DEFECTS LIMIT SERINE SYNTHESIS REQUIRED FOR LUNG CANCER GROWTH AND SURVIVAL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596339. [PMID: 38853873 PMCID: PMC11160605 DOI: 10.1101/2024.05.28.596339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mitochondrial function is important for both energetic and anabolic metabolism. Pathogenic mitochondrial DNA (mtDNA) mutations directly impact these functions, resulting in the detrimental consequences seen in human mitochondrial diseases. The role of pathogenic mtDNA mutations in human cancers is less clear; while pathogenic mtDNA mutations are observed in some cancer types, they are almost absent in others. We report here that the proofreading mutant DNA polymerase gamma ( PolG D256A ) induced a high mtDNA mutation burden in non-small-cell lung cancer (NSCLC), and promoted the accumulation of defective mitochondria, which is responsible for decreased tumor cell proliferation and viability and increased cancer survival. In NSCLC cells, pathogenic mtDNA mutations increased glycolysis and caused dependence on glucose. The glucose dependency sustained mitochondrial energetics but at the cost of a decreased NAD+/NADH ratio that inhibited de novo serine synthesis. Insufficient serine synthesis, in turn, impaired the downstream synthesis of GSH and nucleotides, leading to impaired tumor growth that increased cancer survival. Unlike tumors with intact mitochondrial function, NSCLC with pathogenic mtDNA mutations were sensitive to dietary serine and glycine deprivation. Thus, mitochondrial function in NSCLC is required specifically to sustain sufficient serine synthesis for nucleotide production and redox homeostasis to support tumor growth, explaining why these cancers preserve functional mtDNA. In brief High mtDNA mutation burden in non-small-cell lung cancer (NSCLC) leads to the accumulation of respiration-defective mitochondria and dependency on glucose and glycolytic metabolism. Defective respiratory metabolism causes a massive accumulation of cytosolic nicotinamide adenine dinucleotide + hydrogen (NADH), which impedes serine synthesis and, thereby, glutathione (GSH) and nucleotide synthesis, leading to impaired tumor growth and increased survival. Highlights Proofreading mutations in Polymerase gamma led to a high burden of mitochondrial DNA mutations, promoting the accumulation of mitochondria with respiratory defects in NSCLC.Defective respiration led to reduced proliferation and viability of NSCLC cells increasing survival to cancer.Defective respiration caused glucose dependency to fuel elevated glycolysis.Altered glucose metabolism is associated with high NADH that limits serine synthesis, leading to impaired GSH and nucleotide production.Mitochondrial respiration defects sensitize NSCLC to dietary serine/glycine starvation, further increasing survival. Abstract Figure
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Justin Margret J, Jayasankaran C, Amritkumar P, Azaiez H, Srisailapathy CRS. Unraveling the Genetic Basis of Combined Deafness and Male Infertility Phenotypes through High-Throughput Sequencing in a Unique Cohort from South India. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300206. [PMID: 38884051 PMCID: PMC11170077 DOI: 10.1002/ggn2.202300206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/15/2024] [Indexed: 06/18/2024]
Abstract
The co-occurrence of sensorineural hearing loss and male infertility has been reported in several instances, suggesting potential shared genetic underpinnings. One such example is the contiguous gene deletion of CATSPER2 and STRC genes, previously associated with deafness-infertility syndrome (DIS) in males. Fifteen males with both hearing loss and infertility from southern India after exclusion for the DIS contiguous gene deletion and the FOXI1 gene mutations are subjected to exome sequencing. This resolves the genetic etiology in four probands for both the phenotypes; In the remaining 11 probands, two each conclusively accounted for deafness and male infertility etiologies. Genetic heterogeneity is well reflected in both phenotypes. Four recessive (TRIOBP, SLC26A4, GJB2, COL4A3) and one dominant (SOX10) for the deafness; six recessive genes (LRGUK, DNAH9, ARMC4, DNAH2, RSPH6A, and ACE) for male infertility can be conclusively ascribed. LRGUK and RSPH6A genes are implicated earlier only in mice models, while the ARMC4 gene is implicated in chronic destructive airway diseases due to primary ciliary dyskinesia. This study would be the first to document the role of these genes in the male infertility phenotype in humans. The result suggests that deafness and infertility are independent events and do not segregate together among the probands.
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Affiliation(s)
- Jeffrey Justin Margret
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Department of Pediatrics Louisiana State University Health Sciences Center Shreveport LA 71103 USA
| | - Chandru Jayasankaran
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Department of Personalized Health Care Roche Products India Pvt., Ltd. Bengaluru Karnataka 560 025 India
| | - Pavithra Amritkumar
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Meenakshi Academy of Higher Education and Research (MAHER) Chennai 600 078 India
| | - Hela Azaiez
- Department of Otolaryngology Carver College of Medicine University of Iowa Iowa City Iowa 52242 USA
| | - C R Srikumari Srisailapathy
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
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Aoki T, Nishida N, Kurebayashi Y, Sakai K, Morita M, Chishina H, Takita M, Hagiwara S, Ida H, Ueshima K, Minami Y, Tsurusaki M, Nakai T, Sakamoto M, Nishio K, Kudo M. Two Distinct Characteristics of Immune Microenvironment in Human Hepatocellular Carcinoma with Wnt/β-Catenin Mutations. Liver Cancer 2024; 13:285-305. [PMID: 38894812 PMCID: PMC11185857 DOI: 10.1159/000533818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/22/2023] [Indexed: 06/21/2024] Open
Abstract
Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME was classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells, and myeloid-derived suppressor cell activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Tomoko Aoki
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Naoshi Nishida
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Yutaka Kurebayashi
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Masahiro Morita
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Hirokazu Chishina
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Masahiro Takita
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Satoru Hagiwara
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Hiroshi Ida
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Kazuomi Ueshima
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Yasunori Minami
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Masakatsu Tsurusaki
- Department of Radiology, Kindai University Faculty of Medicine, Osakasayama, Japan
| | - Takuya Nakai
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Michiie Sakamoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Masatoshi Kudo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osakasayama, Japan
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Mozibullah M, Eslampanah Seyedi H, Khatun M, Solayman M. Identification and analysis of oncogenic non-synonymous single nucleotide polymorphisms in the human NRAS gene: An exclusive in silico study. J Genet Eng Biotechnol 2024; 22:100378. [PMID: 38797553 PMCID: PMC11087716 DOI: 10.1016/j.jgeb.2024.100378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND N-ras protein is encoded by the NRAS gene and operates as GDP-GTP-controlled on/off switching. N-ras interacts with cellular signaling networks that regulate various cellular activities including cell proliferation and survival. The nonsynonymous single nucleotide polymorphism (nsSNPs)-mediated alteration can substantially disrupt the structure and activity of the corresponding protein. N-ras has been reported to be associated with numerous diseases including cancers due to the nsSNPs. A comprehensive study on the NRAS gene to unveil the potentially damaging and oncogenic nsSNPs is yet to be accomplished. Hence, this extensive in silico study is intended to identify the disease-associated, specifically oncogenic nsSNPs of the NRAS gene. RESULTS Out of 140 missense variants, 7 nsSNPs (I55R, G60E, G60R, Y64D, L79F, D119G, and V152F) were identified to be damaging utilizing 10 computational tools that works based on different algorithms with high accuracy. Among those, G60E, G60R, and D119G variants were further filtered considering their location in the highly conserved region and later identified as oncogenic variants. Interestingly, G60E and G60R variants were revealed to be particularly associated with lung adenocarcinoma, rhabdomyosarcoma, and prostate adenocarcinoma. Therefore, D119G could be subjected to detailed investigation for identifying its association with specific cancer. CONCLUSION This in silico study identified the deleterious and oncogenic missense variants of the human NRAS gene that could be utilized for designing further experimental investigation. The outcomes of this study would be worthwhile in future research for developing personalized medicine.
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Affiliation(s)
- Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | | | - Marina Khatun
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Solayman
- Department of Biochemistry and Molecular Biology, Primeasia University, Bangladesh.
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Krishnamurthy K, Chai J, Liu X, Wang Y, Naeem R, Goldstein DY. Clinical validation of the Ion Torrent Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer as a stand-alone assay for single-nucleotide variants, insertions/deletions, and fusion genes: Challenges, performance, and perspectives. Am J Clin Pathol 2024:aqae063. [PMID: 38823030 DOI: 10.1093/ajcp/aqae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 04/26/2024] [Indexed: 06/03/2024] Open
Abstract
OBJECTIVES Myeloid neoplasms require comprehensive characterization of genetic abnormalities, including single-nucleotide variants, small insertions and deletions, and fusions and translocations for management. The Oncomine Myeloid Assay GX v2 (Thermo Fisher Scientific) analyzes 17 full genes, 28 hotspot genes, 30 fusion driver genes, and 5 expression genes. METHODS The validation set included 192 DNA samples, 28 RNA samples, and 9 cell lines and contrived controls. The DNA and RNA were extracted from both peripheral blood and bone marrow. Library preparation, templating, and sequencing was performed on the fully automated Genexus Integrated Sequencer (Thermo Fisher Scientific). The sequencing data were analyzed by manual curation, default Oncomine filters and the Oncomine Reporter (Thermo Fisher Scientific). RESULTS Of the 600 reference pathogenic DNA variants targeted by the assay, concordance was seen in 98.3% of unfiltered variant call format files. Precision and reproducibility were 100%, and the lower limit of detection was 2% variant allele frequency for DNA. Inability to detect variants in long homopolymer regions intrinsic to the Ion Torrent chemistry led to 7 missed variants; 100% concordance was seen with reference RNA samples. CONCLUSIONS This extensive clinical validation of the Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer with its built-in bioinformatics pipeline and Ion Torrent Oncomine Reporter shows robust performance in terms of variant calling accuracy, precision, and reproducibility, with the advantage of a rapid turnaround time of 2 days. The greatest limitation is the inability to detect variants in long homopolymer regions.
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Affiliation(s)
| | - Jiani Chai
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Xiaowei Liu
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Yanhua Wang
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - Rizwan Naeem
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
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Xu L, Zhang Y, Guo Y, Chen Q, Zhang M, Chen H, Geng J, Huang X. Whole-genome resequencing uncovers diversity and selective sweep in Kazakh cattle. Anim Genet 2024; 55:377-386. [PMID: 38561945 DOI: 10.1111/age.13425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/07/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
The Kazakh cattle in the Xinjiang Uygur Autonomous Region of China are highly adaptable and have multiple uses, including milk and meat production, and use as draft animals. They are an excellent original breed that could be enhanced by breeding and hybrid improvement. However, the genomic diversity and signature of selection underlying the germplasm characteristics require further elucidation. Herein, we evaluated 26 Kazakh cattle genomes in comparison with 103 genomes of seven other cattle breeds from regions around the world to assess the Kazakh cattle genetic variability. We revealed that the relatively low linkage disequilibrium at large SNP distances was strongly correlated with the largest effective population size among Kazakh cattle. Using population structural analysis, we next demonstrated a taurine lineage with restricted Bos indicus introgression among Kazakh cattle. Notably, we identified putative selected genes associated with resistance to disease and body size within Kazakh cattle. Together, our findings shed light on the evolutionary history and breeding profile of Kazakh cattle, as well as offering indispensable resources for germplasm resource conservation and crossbreeding program implementation.
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Affiliation(s)
- Lei Xu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yunyun Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yang Guo
- Xinjiang Uygur Autonomous Region Animal Husbandry Station, Urumqi, China
| | - Qiuming Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Juan Geng
- Xinjiang Uygur Autonomous Region Animal Husbandry Station, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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García-Aznar JM, Alonso Alvarez S, Bernal Del Castillo T. Pivotal role of BCL11B in the immune, hematopoietic and nervous systems: a review of the BCL11B-associated phenotypes from the genetic perspective. Genes Immun 2024; 25:232-241. [PMID: 38472338 PMCID: PMC11178493 DOI: 10.1038/s41435-024-00263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
The transcription factor BCL11B plays an essential role in the development of central nervous system and T cell differentiation by regulating the expression of numerous genes involved in several pathways. Monoallelic defects in the BCL11B gene leading to loss-of-function are associated with a wide spectrum of phenotypes, including neurological disorders with or without immunological features and susceptibility to hematological malignancies. From the genetic point of view, the landscape of BCL11B mutations reported so far does not fully explain the genotype-phenotype correlation. In this review, we sought to compile the phenotypic and genotypic variables associated with previously reported mutations in this gene in order to provide a better understanding of the consequences of deleterious variants. We also highlight the importance of a careful evaluation of the mutation type, its location and the pattern of inheritance of the variants in order to assign the most accurate pathogenicity and actionability of the genetic findings.
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Affiliation(s)
- José María García-Aznar
- Healthincode, A Coruña, Spain.
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain.
- Health Research Institute of Principado de Asturias, Oviedo, Spain.
| | - Sara Alonso Alvarez
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
| | - Teresa Bernal Del Castillo
- Universitary Institute of Oncology of Principado de Asturias (IUOPA), Oviedo, Spain
- Health Research Institute of Principado de Asturias, Oviedo, Spain
- Hematology Department, Hospital Universitario Clínico de Asturias, Oviedo, Spain
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Roy AS, Feroz T, Islam MK, Munim MA, Supti DA, Antora NJ, Al Reza H, Gosh S, Bahadur NM, Alam MR, Hossain MS. A computational approach for structural and functional analyses of disease-associated mutations in the human CYLD gene. Genomics Inform 2024; 22:4. [PMID: 38907316 PMCID: PMC11184958 DOI: 10.1186/s44342-024-00007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/26/2023] [Indexed: 06/23/2024] Open
Abstract
Tumor suppressor cylindromatosis protein (CYLD) regulates NF-κB and JNK signaling pathways by cleaving K63-linked poly-ubiquitin chain from its substrate molecules and thus preventing the progression of tumorigenesis and metastasis of the cancer cells. Mutations in CYLD can cause aberrant structure and abnormal functionality leading to tumor formation. In this study, we utilized several computational tools such as PANTHER, PROVEAN, PredictSNP, PolyPhen-2, PhD-SNP, PON-P2, and SIFT to find out deleterious nsSNPs. We also highlighted the damaging impact of those deleterious nsSNPs on the structure and function of the CYLD utilizing ConSurf, I-Mutant, SDM, Phyre2, HOPE, Swiss-PdbViewer, and Mutation 3D. We shortlisted 18 high-risk nsSNPs from a total of 446 nsSNPs recorded in the NCBI database. Based on the conservation profile, stability status, and structural impact analysis, we finalized 13 nsSNPs. Molecular docking analysis and molecular dynamic simulation concluded the study with the findings of two significant nsSNPs (R830K, H827R) which have a remarkable impact on binding affinity, RMSD, RMSF, radius of gyration, and hydrogen bond formation during CYLD-ubiquitin interaction. The principal component analysis compared native and two mutants R830K and H827R of CYLD that signify structural and energy profile fluctuations during molecular dynamic (MD) simulation. Finally, the protein-protein interaction network showed CYLD interacts with 20 proteins involved in several biological pathways that mutations can impair. Considering all these in silico analyses, our study recommended conducting large-scale association studies of nsSNPs of CYLD with cancer as well as designing precise medications against diseases associated with these polymorphisms.
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Affiliation(s)
- Arpita Singha Roy
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Tasmiah Feroz
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Kobirul Islam
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Adnan Munim
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Dilara Akhter Supti
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Nusrat Jahan Antora
- Department of Genetic Engineering and Biotechnology, East West University, Dhaka, 1212, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Supriya Gosh
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Mohammad Rahanur Alam
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| | - Md Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
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Werren EA, Peirent ER, Jantti H, Guxholli A, Srivastava KR, Orenstein N, Narayanan V, Wiszniewski W, Dawidziuk M, Gawlinski P, Umair M, Khan A, Khan SN, Geneviève D, Lehalle D, van Gassen KLI, Giltay JC, Oegema R, van Jaarsveld RH, Rafiullah R, Rappold GA, Rabin R, Pappas JG, Wheeler MM, Bamshad MJ, Tsan YC, Johnson MB, Keegan CE, Srivastava A, Bielas SL. Biallelic variants in CSMD1 are implicated in a neurodevelopmental disorder with intellectual disability and variable cortical malformations. Cell Death Dis 2024; 15:379. [PMID: 38816421 PMCID: PMC11140003 DOI: 10.1038/s41419-024-06768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 05/03/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
CSMD1 (Cub and Sushi Multiple Domains 1) is a well-recognized regulator of the complement cascade, an important component of the innate immune response. CSMD1 is highly expressed in the central nervous system (CNS) where emergent functions of the complement pathway modulate neural development and synaptic activity. While a genetic risk factor for neuropsychiatric disorders, the role of CSMD1 in neurodevelopmental disorders is unclear. Through international variant sharing, we identified inherited biallelic CSMD1 variants in eight individuals from six families of diverse ancestry who present with global developmental delay, intellectual disability, microcephaly, and polymicrogyria. We modeled CSMD1 loss-of-function (LOF) pathogenesis in early-stage forebrain organoids differentiated from CSMD1 knockout human embryonic stem cells (hESCs). We show that CSMD1 is necessary for neuroepithelial cytoarchitecture and synchronous differentiation. In summary, we identified a critical role for CSMD1 in brain development and biallelic CSMD1 variants as the molecular basis of a previously undefined neurodevelopmental disorder.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CTt, 06032, USA
| | - Emily R Peirent
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Henna Jantti
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alba Guxholli
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kinshuk Raj Srivastava
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Naama Orenstein
- Schneider Children's Medical Center of Israel, Petah Tikva, 4920235, Israel
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Wojciech Wiszniewski
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Mateusz Dawidziuk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Pawel Gawlinski
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, 11481, Saudi Arabia
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Punjab, 54770, Pakistan
| | - Amjad Khan
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Zoology, University of Lakki Marwat, Lakki Marwat, Khyber Pakhtunkhwa, 28420, Pakistan
| | - Shahid Niaz Khan
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | - David Geneviève
- Montpellier University, Inserm Unit U1183, Reference Center for Rare Diseases and Developmental Anomalies, CHU, 34000, Montpellier, France
| | - Daphné Lehalle
- Sorbonne University, Department of Medical Genetics, Hospital Armand Trousseau, 75012, Paris, France
| | - K L I van Gassen
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, 3584 EA, The Netherlands
| | - Jacques C Giltay
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, 3584 EA, The Netherlands
| | - Renske Oegema
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, 3584 EA, The Netherlands
| | - Richard H van Jaarsveld
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, 3584 EA, The Netherlands
| | - Rafiullah Rafiullah
- Department of Biotechnology, Faculty of Life Sciences, BUITEMS, Quetta, 87300, Pakistan
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University, Heidelberg, 69120, Germany
| | - Rachel Rabin
- Department of Pediatrics, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - John G Pappas
- Department of Pediatrics, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Marsha M Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute, Washington, 98195, USA
| | - Yao-Chang Tsan
- Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew B Johnson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine E Keegan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Anshika Srivastava
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India.
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Chatterjee D, Heeamoni SA, Sultana T, Mou SI, Mostofa MA, Hossain MA, Hosen MI, Faruk MO. Delineating the mechanistic relevance of the TP53 gene and its mutational impact on gene expression and patients' survival in bladder cancer. Heliyon 2024; 10:e31286. [PMID: 38803860 PMCID: PMC11129003 DOI: 10.1016/j.heliyon.2024.e31286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Bladder carcinoma (BLCA) is a widespread urological malignancy causing significant global mortality, often hindered by delayed diagnosis and limited treatments. BLCA frequently exhibits TP53 mutations, playing a pivotal role in its pathogenesis and underscoring the potential of targeting TP53 as a therapeutic approach for this prevalent urological malignancy. Tumor tissues from 50 bladder cancer patients were used for mutational analysis in TP53's mutation-rich exons (5, 7, & 8). The gene expression of the TP53 gene, along with a TP53-target gene B-cell translocation gene 2 (BTG2) was also assessed in the cDNA samples from the same BLCA tissues and 15 urine controls of healthy people. The analysis revealed 22 % of patients with somatic hotspot mutations, 18 % with pathogenic missense mutations, and 12 % with intronic variants. Patients with somatic mutations exhibited the worst prognosis, supported by survival analysis from The Cancer Genome Atlas (TCGA) BLCA data. Interestingly, H296Y missense mutation correlated with higher TP53 expression and improved survival, while intronic SNPs were linked to worse outcomes. Additionally, upregulated BTG2 expression in mutated patients was observed which was correlated with poor prognosis, emphasizing the role of TP53 mutations in bladder cancer progression. The multivariate analysis highlighted the predictive power of TP53 mutations, with a high frequency of high-grade tumors (78.57 %) in mutated patients, underscoring their role in cancer progression. In conclusion, this study emphasizes the crucial role of TP53 mutations in bladder cancer patients from Bangladesh.
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Affiliation(s)
- Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | | | - Tamanna Sultana
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Sadia Islam Mou
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Munshi Akid Mostofa
- Department of Genito-Urinary Oncology, National Institute of Cancer Research & Hospital (NICRH), Mohakhali, Bangladesh
| | - Md Akmal Hossain
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Md Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Md Omar Faruk
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
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Gadhia A, Barker E, Morgan A, Barclay JW. Functional analysis of epilepsy-associated GABA A receptor mutations using Caenorhabditis elegans. Epilepsia Open 2024. [PMID: 38813985 DOI: 10.1002/epi4.12982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/03/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024] Open
Abstract
OBJECTIVE GABAA receptor subunit mutations pose a significant risk for genetic generalized epilepsy; however, there are over 150 identified variants, many with unknown or unvalidated pathogenicity. We aimed to develop in vivo models for testing GABAA receptor variants using the model organism, Caenorhabditis elegans. METHODS CRISPR-Cas9 gene editing was used to create a complete deletion of unc-49, a C. elegans GABAA receptor, and to create homozygous epilepsy-associated mutations in the endogenous unc-49 gene. The unc-49 deletion strain was rescued with transgenes for either the C. elegans unc-49B subunit or the α1, β3, and γ2 subunits for the human GABAA receptor. All newly created strains were analyzed for phenotype and compared against existing unc-49 mutations. RESULTS Nematodes with a full genetic deletion of the entire unc-49 locus were compared with existing unc-49 mutations in three separate phenotypic assays-coordinated locomotion, shrinker frequency and seizure-like convulsions. The full unc-49 deletion exhibited reduced locomotion and increased shrinker frequency and PTZ-induced convulsions, but were not found to be phenotypically stronger than existing unc-49 mutations. Rescue with the unc-49B subunit or creation of humanized worms for the GABAA receptor both showed partial phenotypic rescue for all three phenotypes investigated. Finally, two epilepsy-associated variants were analyzed and deemed to be loss of function, thus validating their pathogenicity. SIGNIFICANCE These findings establish C. elegans as a genetic model to investigate GABAA receptor mutations and delineate a platform for validating associated variants in any epilepsy-associated gene. PLAIN LANGUAGE SUMMARY Epilepsy is a complex human disease that can be caused by mutations in specific genes. Many possible mutations have been identified, but it is unknown for most of them whether they cause the disease. We tested the role of mutations in one specific gene using a small microscopic worm as an animal model. Our results establish this worm as a model for epilepsy and confirm that the two unknown mutations are likely to cause the disease.
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Affiliation(s)
- Ami Gadhia
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool, UK
| | - Eleanor Barker
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool, UK
| | - Alan Morgan
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool, UK
| | - Jeff W Barclay
- Department of Biochemistry, Cell and Systems Biology, ISMIB, University of Liverpool, Liverpool, UK
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Maher SA, AbdAllah NB, Ageeli EA, Riad E, Kattan SW, Abdelaal S, Abdelfatah W, Ibrahim GA, Toraih EA, Awadalla GA, Fawzy MS, Ibrahim A. Impact of Interleukin-17 Receptor A Gene Variants on Asthma Susceptibility and Clinical Manifestations in Children and Adolescents. CHILDREN (BASEL, SWITZERLAND) 2024; 11:657. [PMID: 38929236 PMCID: PMC11202101 DOI: 10.3390/children11060657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024]
Abstract
Several single nucleotide polymorphisms (SNPs) in multiple interleukin receptor genes could be associated with asthma risk and/or phenotype. Interleukin-17 (IL-17) has been implicated in tissue inflammation and autoimmune diseases. As no previous studies have uncovered the potential role of IL17 receptor A (RA) gene variants in asthma risk, we aimed to explore the association of four IL17RA SNPs (i.e., rs4819554A/G, rs879577C/T, rs41323645G/A, and rs4819555C/T) with asthma susceptibility/phenotype in our region. TaqMan allelic discrimination analysis was used to genotype 192 individuals. We found that the rs4819554 G/G genotype significantly reduced disease risk in the codominant (OR = 0.15, 95%CI = 0.05-0.45, p < 0.001), dominant (OR = 0.49, 95%CI = 0.26-0.93, p = 0.028), and recessive (OR = 0.18, 95%CI = 0.07-0.52, p < 0.001) models. Similarly, rs879577 showed reduced disease risk associated with the T allele across all genetic models. However, the A allele of rs41323645 was associated with increased disease risk in all models. The G/A and A/A genotypes have higher ORs of 2.47 (95%CI = 1.19-5.14) and 3.86 (95%CI = 1.62-9.18), respectively. Similar trends are observed in the dominant 2.89 (95%CI = 1.47-5.68, p = 0.002) and recessive 2.34 (95%CI = 1.10-4.98, p = 0.025) models. For the rs4819555 variant, although there was no significant association identified under any models, carriers of the rs4819554*A demonstrated an association with a positive family history of asthma (71.4% in carriers vs. 27% in non-carriers; p = 0.025) and the use of relievers for >2 weeks (52.2% of carriers vs. 28.8% of non-carriers; p = 0.047). Meanwhile, the rs4819555*C carriers displayed a significant divergence in the asthma phenotype, specifically atopic asthma (83.3% vs. 61.1%; p = 0.007), showed a higher prevalence of chest tightness (88.9% vs. 61.5%; p = 0.029), and were more likely to report comorbidities (57.7% vs. 16.7%, p = 0.003). The most frequent haplotype in the asthma group was ACAC, with a frequency of 22.87% vs. 1.36% in the controls (p < 0.001). In conclusion, the studied IL17RA variants could be essential in asthma susceptibility and phenotype in children and adolescents.
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Affiliation(s)
- Shymaa Ahmed Maher
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Center of Excellence in Molecular and Cellular Medicine (CEMCM), Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Nouran B. AbdAllah
- Department of Pediatrics, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.B.A.); (S.A.); (A.I.)
| | - Essam Al Ageeli
- Department of Basic Medical Sciences, Faculty of Medicine, Jazan University, Jazan 45141, Saudi Arabia;
| | - Eman Riad
- Department of Chest Diseases and Tuberculosis, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (E.R.); (W.A.)
| | - Shahad W. Kattan
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu 46423, Saudi Arabia;
| | - Sherouk Abdelaal
- Department of Pediatrics, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.B.A.); (S.A.); (A.I.)
| | - Wagdy Abdelfatah
- Department of Chest Diseases and Tuberculosis, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (E.R.); (W.A.)
| | - Gehan A. Ibrahim
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Eman A. Toraih
- Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Medical Genetics Unit, Department of Histology and Cell Biology, Suez Canal University, Ismailia 41522, Egypt
| | - Ghada A. Awadalla
- Biochemistry Department, Animal Health Research Institute, Mansoura Branch, Giza 12618, Egypt;
| | - Manal S. Fawzy
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar P.O. Box 1321, Saudi Arabia
| | - Ahmed Ibrahim
- Department of Pediatrics, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.B.A.); (S.A.); (A.I.)
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Chen R, Lukianova E, van der Loeff IS, Spegarova JS, Willet JDP, James KD, Ryder EJ, Griffin H, IJspeert H, Gajbhiye A, Lamoliatte F, Marin-Rubio JL, Woodbine L, Lemos H, Swan DJ, Pintar V, Sayes K, Ruiz-Morales ER, Eastham S, Dixon D, Prete M, Prigmore E, Jeggo P, Boyes J, Mellor A, Huang L, van der Burg M, Engelhardt KR, Stray-Pedersen A, Erichsen HC, Gennery AR, Trost M, Adams DJ, Anderson G, Lorenc A, Trynka G, Hambleton S. NUDCD3 deficiency disrupts V(D)J recombination to cause SCID and Omenn syndrome. Sci Immunol 2024; 9:eade5705. [PMID: 38787962 DOI: 10.1126/sciimmunol.ade5705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Inborn errors of T cell development present a pediatric emergency in which timely curative therapy is informed by molecular diagnosis. In 11 affected patients across four consanguineous kindreds, we detected homozygosity for a single deleterious missense variant in the gene NudC domain-containing 3 (NUDCD3). Two infants had severe combined immunodeficiency with the complete absence of T and B cells (T -B- SCID), whereas nine showed classical features of Omenn syndrome (OS). Restricted antigen receptor gene usage by residual T lymphocytes suggested impaired V(D)J recombination. Patient cells showed reduced expression of NUDCD3 protein and diminished ability to support RAG-mediated recombination in vitro, which was associated with pathologic sequestration of RAG1 in the nucleoli. Although impaired V(D)J recombination in a mouse model bearing the homologous variant led to milder immunologic abnormalities, NUDCD3 is absolutely required for healthy T and B cell development in humans.
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Affiliation(s)
- Rui Chen
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Elena Lukianova
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Ina Schim van der Loeff
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | | | - Joseph D P Willet
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kieran D James
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Edward J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Helen Griffin
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Akshada Gajbhiye
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Frederic Lamoliatte
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Jose L Marin-Rubio
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Henrique Lemos
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Swan
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Valeria Pintar
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kamal Sayes
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | | | - Simon Eastham
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Penny Jeggo
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Joan Boyes
- Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, UK
| | - Andrew Mellor
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lei Huang
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Karin R Engelhardt
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo 0424, Norway
| | - Hans Christian Erichsen
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo 0424, Norway
| | - Andrew R Gennery
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Anna Lorenc
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
- Open Targets, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
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Rosenfeld E, Mitteer LM, Boodhansingh K, Sanders VR, McKnight H, De Leon DD. Clinical and Molecular Characterization of Hyperinsulinism in Kabuki Syndrome. J Endocr Soc 2024; 8:bvae101. [PMID: 38859884 PMCID: PMC11163021 DOI: 10.1210/jendso/bvae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Indexed: 06/12/2024] Open
Abstract
Context Kabuki syndrome (KS) is associated with congenital hyperinsulinism (HI). Objective To characterize the clinical and molecular features of HI in children with KS. Design Retrospective cohort study of children with KS and HI evaluated between 1998 and 2023. Setting The Congenital Hyperinsulinism Center of the Children's Hospital of Philadelphia. Patients Thirty-three children with KS and HI. Main Outcome Measures HI presentation, treatment, course, and genotype. Results Hypoglycemia was recognized on the first day of life in 25 children (76%). Median age at HI diagnosis was 1.8 months (interquartile range [IQR], 0.6-6.1 months). Median age at KS diagnosis was 5 months (IQR, 2-14 months). Diagnosis of HI preceded KS diagnosis in 20 children (61%). Twenty-four children (73%) had a pathogenic variant in KMT2D, 5 children (15%) had a pathogenic variant in KDM6A, and 4 children (12%) had a clinical diagnosis of KS. Diazoxide trial was conducted in 25 children, 92% of whom were responsive. HI treatment was discontinued in 46% of the cohort at median age 2.8 years (IQR, 1.3-5.7 years). Conclusion Hypoglycemia was recognized at birth in most children with KS and HI, but HI diagnosis was often delayed. HI was effectively managed with diazoxide in most children. In contrast to prior reports, the frequency of variants in KMT2D and KDM6A were similar to their overall prevalence in individuals with KS. Children diagnosed with KS should undergo evaluation for HI, and, because KS features may not be recognized in infancy, KMT2D and KDM6A should be included in the genetic evaluation of HI.
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Affiliation(s)
- Elizabeth Rosenfeld
- Congenital Hyperinsulinism Center, Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren M Mitteer
- Congenital Hyperinsulinism Center, Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kara Boodhansingh
- Congenital Hyperinsulinism Center, Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Victoria R Sanders
- Congenital Hyperinsulinism Center, Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Heather McKnight
- Congenital Hyperinsulinism Center, Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Diva D De Leon
- Congenital Hyperinsulinism Center, Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Kamal MM, Mia MS, Faruque MO, Rabby MG, Islam MN, Talukder MEK, Wani TA, Rahman MA, Hasan MM. In silico functional, structural and pathogenicity analysis of missense single nucleotide polymorphisms in human MCM6 gene. Sci Rep 2024; 14:11607. [PMID: 38773180 PMCID: PMC11109216 DOI: 10.1038/s41598-024-62299-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024] Open
Abstract
Single nucleotide polymorphisms (SNPs) are one of the most common determinants and potential biomarkers of human disease pathogenesis. SNPs could alter amino acid residues, leading to the loss of structural and functional integrity of the encoded protein. In humans, members of the minichromosome maintenance (MCM) family play a vital role in cell proliferation and have a significant impact on tumorigenesis. Among the MCM members, the molecular mechanism of how missense SNPs of minichromosome maintenance complex component 6 (MCM6) contribute to DNA replication and tumor pathogenesis is underexplored and needs to be elucidated. Hence, a series of sequence and structure-based computational tools were utilized to determine how mutations affect the corresponding MCM6 protein. From the dbSNP database, among 15,009 SNPs in the MCM6 gene, 642 missense SNPs (4.28%), 291 synonymous SNPs (1.94%), and 12,500 intron SNPs (83.28%) were observed. Out of the 642 missense SNPs, 33 were found to be deleterious during the SIFT analysis. Among these, 11 missense SNPs (I123S, R207C, R222C, L449F, V456M, D463G, H556Y, R602H, R633W, R658C, and P815T) were found as deleterious, probably damaging, affective and disease-associated. Then, I123S, R207C, R222C, V456M, D463G, R602H, R633W, and R658C missense SNPs were found to be highly harmful. Six missense SNPs (I123S, R207C, V456M, D463G, R602H, and R633W) had the potential to destabilize the corresponding protein as predicted by DynaMut2. Interestingly, five high-risk mutations (I123S, V456M, D463G, R602H, and R633W) were distributed in two domains (PF00493 and PF14551). During molecular dynamics simulations analysis, consistent fluctuation in RMSD and RMSF values, high Rg and hydrogen bonds in mutant proteins compared to wild-type revealed that these mutations might alter the protein structure and stability of the corresponding protein. Hence, the results from the analyses guide the exploration of the mechanism by which these missense SNPs of the MCM6 gene alter the structural integrity and functional properties of the protein, which could guide the identification of ways to minimize the harmful effects of these mutations in humans.
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Affiliation(s)
- Md Mostafa Kamal
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Sohel Mia
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Omar Faruque
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Golam Rabby
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Numan Islam
- Department of Food Engineering, North Pacific International University of Bangladesh, Dhaka, Bangladesh
| | | | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - M Atikur Rahman
- Department of Biological Sciences, Alabama State University, 915 S Jackson St, Montgomery, AL, 36104, USA.
| | - Md Mahmudul Hasan
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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Lee JY, Moon J, Hu HJ, Ryu CS, Ko EJ, Ahn EH, Kim YR, Kim JH, Kim NK. Discovery of Pathogenic Variants Associated with Idiopathic Recurrent Pregnancy Loss Using Whole-Exome Sequencing. Int J Mol Sci 2024; 25:5447. [PMID: 38791485 PMCID: PMC11121708 DOI: 10.3390/ijms25105447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Idiopathic recurrent pregnancy loss (RPL) is defined as at least two pregnancy losses before 20 weeks of gestation. Approximately 5% of pregnant couples experience idiopathic RPL, which is a heterogeneous disease with various causes including hormonal, chromosomal, and intrauterine abnormalities. Although how pregnancy loss occurs is still unknown, numerous biological factors are associated with the incidence of pregnancy loss, including genetic variants. Whole-exome sequencing (WES) was conducted on blood samples from 56 Korean patients with RPL and 40 healthy controls. The WES data were aligned by means of bioinformatic analysis, and the detected variants were annotated using machine learning tools to predict the pathogenicity of protein alterations. Each indicated variant was confirmed using Sanger sequencing. A replication study was also conducted in 112 patients and 114 controls. The Variant Effect Scoring Tool, Combined Annotation Dependent Depletion tool, Sorting Intolerant from Tolerant annotation tool, and various databases detected 10 potential variants previously associated with spontaneous abortion genes in patients by means of a bioinformatic analysis of WES data. Several variants were detected in more than one patient. Interestingly, several of the detected genes were functionally clustered, including some with a secretory function (mucin 4; MUC4; rs200737893 G>A and hyaluronan-binding protein 2; HABP2; rs542838125 G>T), in which growth arrest-specific 2 Like 2 (GAS2L2; rs140842796 C>T) and dynamin 2 (DNM2; rs763894364 G>A) are functionally associated with cell protrusion and the cytoskeleton. ATP Binding Cassette Subfamily C Member 6 (ABCC6) was the only gene with two variants. HABP2 (rs542838125 G>T), MUC4 (rs200737893 G>A), and GAS2L2 (rs140842796 C>T) were detected in only the patient group in the replication study. The combination of WES and machine learning tools is a useful method to detect potential variants associated with RPL. Using bioinformatic tools, we found 10 potential variants in 9 genes. WES data from patients are needed to better understand the causes of RPL.
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Affiliation(s)
- Jeong Yong Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
| | - JaeWoo Moon
- Endomics, Inc., Seongnam-si 13595, Republic of Korea; (J.M.); (H.-J.H.)
| | - Hae-Jin Hu
- Endomics, Inc., Seongnam-si 13595, Republic of Korea; (J.M.); (H.-J.H.)
| | - Chang Soo Ryu
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
| | - Eun Ju Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
| | - Eun Hee Ahn
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13596, Republic of Korea; (E.H.A.); (Y.R.K.)
| | - Young Ran Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13596, Republic of Korea; (E.H.A.); (Y.R.K.)
| | - Ji Hyang Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13596, Republic of Korea; (E.H.A.); (Y.R.K.)
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (J.Y.L.); (C.S.R.); (E.J.K.)
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47
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Garg P, Jamal F, Srivastava P. RNA-Seq data analysis reveals novel nonsense mutations in the NPR3 gene leading to the progression of intellectual disability disorder. Heliyon 2024; 10:e30755. [PMID: 38765165 PMCID: PMC11101858 DOI: 10.1016/j.heliyon.2024.e30755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Intellectual disability (ID) is a progressive disorder that affects around 1-3% of the world's population. The heterogeneity of intellectual disability makes it difficult to diagnose as a complete disease. Genetic factors and major mutations play a noticeable role in the development and progression of ID. There is a high need to explore novel variants that may lead to new insights into the progressive aspects of ID. In the current course of study, 31 samples of ID from different studies available on GEO (GSE77742, GSE74263, GSE90682, GSE98476, GSE108887, GSE145710, and PRJEB21964) datasets were taken for the study. These datasets were analyzed for differential gene expression and single nucleotide polymorphism (SNPs). The SNPs of high impact were compared with the differentially expressed genes. Comparison leads to the identification of the priority gene ie NPR3 gene. The identified priority gene further was evaluated for the effect of the mutation using a Mutation Taster. Structure comparison analysis of the wild and mutated proteins of the NPR3 gene was further carried out by UCSF Chimera. Structural analysis reveals the anomalies in protein expression affecting the regulations of the NPR3 gene. These findings identified a novel nonsense mutation (E222*) in the downregulated NPR3 gene that leads to anomalies in the regulation of its protein expression. This missense mutation reveals a major role in causing ID. Our study concludes that the decrease in the expression of the NPR3 gene causes delayed sensory, motor, and physiological functions of the human brain leading to neurodevelopmental delay that causes ID.
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Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, UP, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
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Thongkumkoon P, Sangphukieo A, Tongjai S, Noisagul P, Sangkhathat S, Laochareonsuk W, Kamolphiwong R, Budprom P, Teeyakasem P, Yongpitakwattana P, Thepbundit V, Sirikaew N, Klangjorhor J, Settakorn J, Moonmuang S, Suksakit P, Pasena A, Chaijaruwanich J, Yathongkhum W, Dissook S, Pruksakorn D, Chaiyawat P. Establishment, characterization, and genetic profiling of patient-derived osteosarcoma cells from a patient with retinoblastoma. Sci Rep 2024; 14:11056. [PMID: 38744935 PMCID: PMC11094034 DOI: 10.1038/s41598-024-60628-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Osteosarcoma is the most common malignant bone cancer in pediatric patients. Patients who respond poorly to chemotherapy experience worse clinical outcomes with a high mortality rate. The major challenge is the lack of effective drugs for these patients. To introduce new drugs for clinical approval, preclinical studies based on in vitro models must demonstrate the potency of the tested drugs, enabling the drugs to enter phase 1 clinical trials. Patient-derived cell culture is a promising testing platform for in vitro studies, as they more accurately recapitulate cancer states and genetic profiles compared to cell lines. In the present study, we established patient-derived osteosarcoma cells (PDC) from a patient who had previously been diagnosed with retinoblastoma. We identified a new variant of a germline mutation in the RB1 gene in the tissue of the patient. The biological effects of this PDC were studied to observe whether the cryopreserved PDC retained a feature of fresh PDC. The cryopreserved PDC preserved the key biological effects, including cell growth, invasive capability, migration, and mineralization, that define the conserved phenotypes compared to fresh PDC. From whole genome sequencing analysis of osteosarcoma tissue and patient-derived cells, we found that cryopreserved PDC was a minor population in the origin tissue and was selectively grown under the culture conditions. The cryopreserved PDC has a high resistance to conventional chemotherapy. This study demonstrated that the established cryopreserved PDC has the aggressive characteristics of osteosarcoma, in particular the chemoresistance phenotype that might be used for further investigation in the chemoresistant mechanism of osteosarcoma. In conclusion, the approach we applied for primary cell culture might be a promising method to generate in vitro models for functional testing of osteosarcoma.
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Affiliation(s)
- Patcharawadee Thongkumkoon
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Apiwat Sangphukieo
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Siripong Tongjai
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pitiporn Noisagul
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Surasak Sangkhathat
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
- Translational Medicine Research Center, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
| | - Wison Laochareonsuk
- Division of Surgery, Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
- Translational Medicine Research Center, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
| | - Rawikant Kamolphiwong
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Piyaporn Budprom
- Faculty of Medicine, Musculoskeletal Science and Translational Research (MSTR) Center, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pimpisa Teeyakasem
- Faculty of Medicine, Musculoskeletal Science and Translational Research (MSTR) Center, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Petlada Yongpitakwattana
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Viraporn Thepbundit
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, 10 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Nutnicha Sirikaew
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, 10 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Jeerawan Klangjorhor
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
- Faculty of Medicine, Musculoskeletal Science and Translational Research (MSTR) Center, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jongkolnee Settakorn
- Department of Pathology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sutpirat Moonmuang
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
- Office of Research Administration, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Pathacha Suksakit
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Arnat Pasena
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand
| | - Jeerayut Chaijaruwanich
- Department of Computer Science, Faculty of Science, Data Science Research Center, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wilawan Yathongkhum
- Department of Computer Science, Faculty of Science, Data Science Research Center, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sivamoke Dissook
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, 10 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand.
| | - Dumnoensun Pruksakorn
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand.
- Faculty of Medicine, Musculoskeletal Science and Translational Research (MSTR) Center, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand.
| | - Parunya Chaiyawat
- Faculty of Medicine, Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Chiang Mai University, 110 Intawaroros Road, Si Phum, Muang, Chiang Mai, 50200, Thailand.
- Faculty of Medicine, Musculoskeletal Science and Translational Research (MSTR) Center, Chiang Mai University, Chiang Mai, 50200, Thailand.
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49
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Montanucci L, Brünger T, Bhattarai N, Boßelmann CM, Kim S, Allen JP, Zhang J, Klöckner C, Fariselli P, May P, Lemke JR, Myers SJ, Yuan H, Traynelis SF, Lal D. Distances from ligands as main predictive features for pathogenicity and functional effect of variants in NMDA receptors. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.06.24306939. [PMID: 38766179 PMCID: PMC11100844 DOI: 10.1101/2024.05.06.24306939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variants in genes GRIN1 , GRIN2A , GRIN2B , and GRIN2D , which encode subunits of the N-methyl-D-aspartate receptor (NMDAR), have been associated with severe and heterogeneous neurologic diseases. Missense variants in these genes can result in gain or loss of the NMDAR function, requiring opposite therapeutic treatments. Computational methods that predict pathogenicity and molecular functional effects are therefore crucial for accurate diagnosis and therapeutic applications. We assembled missense variants: 201 from patients, 631 from general population, and 159 characterized by electrophysiological readouts showing whether they can enhance or reduce the receptor function. This includes new functional data from 47 variants reported here, for the first time. We found that pathogenic/benign variants and variants that increase/decrease the channel function were distributed unevenly on the protein structure, with spatial proximity to ligands bound to the agonist and antagonist binding sites being key predictive features. Leveraging distances from ligands, we developed two independent machine learning-based predictors for NMDAR missense variants: a pathogenicity predictor which outperforms currently available predictors (AUC=0.945, MCC=0.726), and the first binary predictor of molecular function (increase or decrease) (AUC=0.809, MCC=0.523). Using these, we reclassified variants of uncertain significance in the ClinVar database and refined a previous genome-informed epidemiological model to estimate the birth incidence of molecular mechanism-defined GRIN disorders. Our findings demonstrate that distance from ligands is an important feature in NMDARs that can enhance variant pathogenicity prediction and enable functional prediction. Further studies with larger numbers of phenotypically and functionally characterized variants will enhance the potential clinical utility of this method.
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50
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Shiv R, Rakeswari, Farjana N, Subbiah U, Ajith A, Balaji A, Mohanasatheesh S. Characterization of missense nonsynonymous single-nucleotide polymorphism of runt-related transcription factor-2 gene - An in silico approach. Indian J Pharmacol 2024; 56:198-205. [PMID: 39078184 DOI: 10.4103/ijp.ijp_533_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 06/04/2024] [Indexed: 07/31/2024] Open
Abstract
OBJECTIVES Single-nucleotide polymorphism (SNP) codes for multiple amino acids, impacting protein functions and disease prognosis. Runt-related transcription factor-2 (RUNX2), a transcription factor linked to osteoblast differentiation, regulates cell proliferation in endothelium and osteoblastic cells. Understanding Runx2's role in nonosseous tissues is rapidly advancing. This study aims to identify harmful SNPs of the RUNX2 gene that may alter disease susceptibility using computational techniques. METHODS The study uses various in silico methods to identify nonsynonymous SNPs (nsSNPs) of the RUNX2 gene, which could potentially alter protein structure and functions, with further analyses by I-Mutant, ConSurf, Netsurf 3.0, GeneMANIA, and Have (y)Our Protein Explained. RESULTS Six missense nsSNPs were identified as potentially harmful, disease-causing, and damaging. Four were found to be unstable, while five were conserved. All six nsSNPs had a coiled secondary structure. Five nsSNPs were found to be destabilized. CONCLUSION The RUNX2 gene's deleterious missense nsSNPs were identified by this study, and they may be exploited in future experimental studies. These high-risk nsSNPs might be considered target molecules in therapeutic and diagnostic therapies in teeth and bone development.
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Affiliation(s)
- Ragul Shiv
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Rakeswari
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Nilofer Farjana
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Usha Subbiah
- Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Athira Ajith
- Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Anitha Balaji
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - S Mohanasatheesh
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
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