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Rehman G, Kashyap J, Srivastav AK, Rizvi S, Kumar U, Tyagi RK. Truncated variants of thyroid hormone receptor beta display disease-inflicting malfunctioning at cellular level. Exp Cell Res 2024; 437:114017. [PMID: 38555013 DOI: 10.1016/j.yexcr.2024.114017] [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: 01/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
Thyroid hormone receptor β (THRβ) is a member of the nuclear receptor superfamily of ligand-modulated transcription factors. Upon ligand binding, THRβ sequentially recruits the components of transcriptional machinery to modulate target gene expression. In addition to regulating diverse physiological processes, THRβ plays a crucial role in hypothalamus-pituitary-thyroid axis feedback regulation. Anomalies in THRβ gene/protein structure are associated with onset of diverse disease states. In this study, we investigated disease-inflicting truncated variants of THRβ using in-silico analysis and cell-based assays. We examined the THRβ truncated variants on multiple test parameters, including subcellular localization, ligand-receptor interactions, transcriptional functions, interaction with heterodimeric partner RXR, and receptor-chromatin interactions. Moreover, molecular dynamic simulation approaches predicted that shortened THRβ-LBD due to point mutations contributes proportionally to the loss of structural integrity and receptor stability. Deviant subcellular localization and compromised transcriptional function were apparent with these truncated variants. Present study shows that 'mitotic bookmarking' property of some THRβ variants is also affected. The study highlights that structural and conformational attributes of THRβ are necessary for normal receptor functioning, and any deviations may contribute to the underlying cause of the inflicted diseases. We anticipate that insights derived herein may contribute to improved mechanistic understanding to assess disease predisposition.
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Affiliation(s)
- Ghausiya Rehman
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Jyoti Kashyap
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Amit Kumar Srivastav
- School of Nano Sciences, Central University of Gujarat, Gandhinagar, Gujarat, 382030, India
| | - Sheeba Rizvi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Umesh Kumar
- School of Nano Sciences, Central University of Gujarat, Gandhinagar, Gujarat, 382030, India; Nutrition Biology Department, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
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Liao Z, Zhang Q, Yang L, Li H, Mo W, Song Z, Huang X, Wen S, Cheng X, He M. Increased hsa-miR-100-5p Expression Improves Hepatocellular Carcinoma Prognosis in the Asian Population with PLK1 Variant rs27770A>G. Cancers (Basel) 2023; 16:129. [PMID: 38201556 PMCID: PMC10778516 DOI: 10.3390/cancers16010129] [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: 09/26/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) has the highest incidence and mortality in the Asian population, and race is an independent risk factor affecting survival time in liver cancer. Micro RNAs (miRNAs) are remarkably dysregulated in HCC and closely associated with HCC prognosis. Recent studies show that genetic variability between ethnic groups may result in differences in the specificity of HCC miRNA biomarkers. Here, we reveal a high expression level of hsa-miR-100-5p, an HCC prognosis-related miRNA, which improves HCC prognosis in the Asian Population with Polo-like kinase 1 (PLK1) variant rs27770A>G. In this study, we discovered that hsa-miR-100-5p was downregulated in various HCC cell lines. While mimics transient transfection and mouse liver cancer model confirmed the interaction between hsa-miR-100-5p and PLK1, a stratified analysis based on the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) data suggest both low hsa-miR-100-5p expression level and high PLK1 expression level associated with poor HCC prognosis, especially in the Asian population. According to the 1000 Genomes Project database, the SNP rs27770 located in 3'UTR of PLK1 had a significantly higher G allele frequency in the East Asian population. Bioinformatics analysis suggested that rs27770 A>G affects PLK1 mRNA secondary structure and alters the hsa-miR-100-5p/PLK1 interaction by forming an additional seedless binding site. This racial variation caused PLK1 to be more vulnerable to hsa-miR-100-5p inhibition, resulting in hsa-miR-100-5p being more favorable for HCC prognosis in the Asian population.
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Affiliation(s)
- Zhouxiang Liao
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Qi Zhang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Lichao Yang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Hui Li
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Wanling Mo
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Zhenyu Song
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Xuejing Huang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Sha Wen
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Xiaojing Cheng
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Life Sciences Institute, Guangxi Medical University, Nanning 530021, China
| | - Min He
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning 530021, China
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Rizvi S, Chhabra A, Tripathi A, Tyagi RK. Mitotic genome-bookmarking by nuclear hormone receptors: A novel dimension in epigenetic reprogramming and disease assessment. Mol Cell Endocrinol 2023; 578:112069. [PMID: 37730146 DOI: 10.1016/j.mce.2023.112069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
Arrival of multi-colored fluorescent proteins and advances in live cell imaging has immensely contributed to our understanding of intracellular trafficking of nuclear receptors and their roles in gene regulatory functions. These regulatory events need to be faithfully propagated from progenitor to progeny cells. This is corroborated by multiple converging mechanisms that include histone modifications and lately, the phenomenon of 'mitotic genome-bookmarking' by specific transcription factors. This phenomenon refers to the retention and feed-forward transmission of progenitor's architectural blueprint of active transcription status which is silenced and preserved during mitosis. Upon mitotic exit, this phenomenon ensures accurate reactivation of transcriptome, proteome, cellular traits and phenotypes in the progeny cells. In addition to diverse modes of genome-bookmarking by nuclear receptors, a correlation between disease-associated receptor polymorphism and disruption of this phenomenon is apparent. However, breakthrough technologies shall reveal finer details of this phenomenon to help achieve normalcy in receptor-specific diseases.
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Affiliation(s)
- Sheeba Rizvi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ayushi Chhabra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Anjali Tripathi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, 110067, India.
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Liu J, Rahim F, Zhou J, Fan S, Jiang H, Yu C, Chen J, Xu J, Yang G, Shah W, Zubair M, Khan A, Li Y, Shah B, Zhao D, Iqbal F, Jiang X, Guo T, Xu P, Xu B, Wu L, Ma H, Zhang Y, Zhang H, Shi Q. Loss-of-function variants in KCTD19 cause non-obstructive azoospermia in humans. iScience 2023; 26:107193. [PMID: 37485353 PMCID: PMC10362269 DOI: 10.1016/j.isci.2023.107193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/19/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Azoospermia is a significant cause of male infertility, with non-obstructive azoospermia (NOA) being the most severe type of spermatogenic failure. NOA is mostly caused by congenital factors, but our understanding of its genetic causes is very limited. Here, we identified a frameshift variant (c.201_202insAC, p.Tyr68Thrfs∗17) and two nonsense variants (c.1897C>T, p.Gln633∗; c.2005C>T, p.Gln669∗) in KCTD19 (potassium channel tetramerization domain containing 19) from two unrelated infertile Chinese men and a consanguineous Pakistani family with three infertile brothers. Testicular histological analyses revealed meiotic metaphase I (MMI) arrest in the affected individuals. Mice modeling KCTD19 variants recapitulated the same MMI arrest phenotype due to severe disrupted individualization of MMI chromosomes. Further analysis showed a complete loss of KCTD19 protein in both Kctd19 mutant mouse testes and affected individual testes. Collectively, our findings demonstrate the pathogenicity of the identified KCTD19 variants and highlight an essential role of KCTD19 in MMI chromosome individualization.
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Affiliation(s)
- Junyan Liu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Fazal Rahim
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Jianteng Zhou
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Suixing Fan
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Hanwei Jiang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Changping Yu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Jing Chen
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Jianze Xu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Gang Yang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Wasim Shah
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Muhammad Zubair
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Asad Khan
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Yang Li
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Basit Shah
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Daren Zhao
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Furhan Iqbal
- Institute of Pure and Applied Biology, Zoology Division, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Xiaohua Jiang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Tonghang Guo
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Peng Xu
- Hainan Jinghua Hejing Hospital for Reproductive Medicine, Hainan 570125, China
| | - Bo Xu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Limin Wu
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Hui Ma
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Yuanwei Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Huan Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Qinghua Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Research Center for Physical Sciences at the Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
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Jiang F, Yin X, Li ZW, Guo R, Wang J, Fan J, Zhang Y, Kang MS, Fan X. Predicting heterosis via genetic distance and the number of SNPs in selected segments of chromosomes in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1111961. [PMID: 36875600 PMCID: PMC9982102 DOI: 10.3389/fpls.2023.1111961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
A reliable method is needed for predicting heterosis to help maize (Zea mays L.) breeders develop new hybrids more efficiently. The objectives of this study were to 1) investigate if the numbers of selected PEUS SNPs (the SNP in the Promoters (1 kb upstream of the start codon), Exons, Untranslated region (UTR), and Stop codons) could be used for predicting MPH or BPH of GY; 2) if the number of PEUS SNPs is a better predictor of MPH and/or BPH of GY than genetic distance (GD). A line × tester experiment was conducted with 19 elite maize inbreds from three heterotic groups, which were crossed with five testers. The multi-location trial data on GY were recorded. Whole-genome resequencing of the 24 inbreds was carried out. After filtration, a total of 58,986,791 SNPs were called with high confidence. Selected SNPs in the promoters, exons, untranslated region (UTRs), and stop codons (PEUS SNPs) were counted, and the GD was calculated. The correlation between heterozygous PEUS SNPs/GD and mean MPH, BPH of GY revealed that 1) both the number of heterozygous PEUS SNP and the GD were highly correlated to both MPH_GY and BPH_GY at p<0.01 with correlation coefficients for the number of heterozygous PEUS SNP being higher than that for GD; 2) the mean number of heterozygous PEUS SNPs was also highly correlated with mean BPH_GY or mean MPH_GY (p<0.05) in the 95 crosses grouped by either male or female parents, implying that inbreds can be selected before making the actual crosses in the field. We concluded that the number of heterozygous PEUS SNPs would be a better predictor of MPH_GY and BPH_GY than GD. Hence, maize breeders could use heterozygous PEUS SNPs to select inbreds with high heterosis potential before actually making the crosses, thus improving the breeding efficiency.
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Affiliation(s)
- Fuyan Jiang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - XingFu Yin
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Zi Wei Li
- Yunnan Dehong Dai and Jingpo Nationality Institute of Agricultural Sciences, Mangshi, Yunnan, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Jing Wang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Jun Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Manjit S. Kang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
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Solanki S, Kumar V, Kashyap P, Kumar R, De S, Datta TK. Beta-defensins as marker for male fertility: a comprehensive review†. Biol Reprod 2023; 108:52-71. [PMID: 36322147 DOI: 10.1093/biolre/ioac197] [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: 06/29/2022] [Revised: 10/15/2022] [Accepted: 10/21/2022] [Indexed: 12/05/2022] Open
Abstract
Bovine male fertility in animals has a direct impact on the productivity of dairy herds. The epididymal sperm maturations involve extensive sperm surface modifications to gain the fertilizing ability, especially by absorptions of the plethora of biomolecules, including glycoprotein beta-defensins (BDs), enzymes, organic ions, protein, and phospholipids. Defensins are broad-range nonspecific antimicrobial peptides that exhibit strong relations with innate and adaptive immunity, but their roles in male fertility are relatively recently identified. In the course of evolution, BD genes give rise to different clusters with specific functions, especially reproductive functions, by undergoing duplications and nonsynonymous mutations. BD polymorphisms have been reported with milk compositions, disease resistance, and antimicrobial activities. However, in recent decades, the link of BD polymorphisms with fertility has emerged as an appealing improvement of reproductive performance such as sperm motility, membrane integrity, cervical mucus penetration, evading of uterus immunosurveillance, oviduct cell attachment, and egg recognition. The reproductive-specific glycosylated BD class-A BDs (CA-BDs) have shown age- and sex-specific expressions in male reproductive organs, signifying their physiological pleiotropism, especially in the sperm maturation and sperm transport in the female reproductive tract. By considering adult male reproductive organ-specific BD expressions, importance in sperm functionalities, and bioinformatic analysis, we have selected two bovine BBD126 and BBD129 genes as novel potential biomarkers of bovine male fertility. Despite the importance of BDs, however, genomic characterization of most BD genes across most livestock and nonmodel organisms remains predictive/incomplete. The current review discusses our understanding of BD pleiotropic functions, polymorphism, and genomic structural attributes concerning the fertilizability of the male gamete in dairy animals.
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Affiliation(s)
- Subhash Solanki
- Animal Genomics Lab, National Dairy Research Institute, Karnal, India
| | - Vijay Kumar
- NMR lab-II, National Institute of immunology, New Delhi, India
| | - Poonam Kashyap
- Animal Genomics Lab, National Dairy Research Institute, Karnal, India
| | - Rakesh Kumar
- Animal Genomics Lab, National Dairy Research Institute, Karnal, India
| | - Sachinandan De
- Animal Genomics Lab, National Dairy Research Institute, Karnal, India
| | - Tirtha Kumar Datta
- Animal Genomics Lab, National Dairy Research Institute, Karnal, India.,ICAR- Central Institute for Research on Buffaloes, Hisar, India
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Wienert B, Cromer MK. CRISPR nuclease off-target activity and mitigation strategies. Front Genome Ed 2022; 4:1050507. [PMID: 36439866 PMCID: PMC9685173 DOI: 10.3389/fgeed.2022.1050507] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
The discovery of CRISPR has allowed site-specific genomic modification to become a reality and this technology is now being applied in a number of human clinical trials. While this technology has demonstrated impressive efficacy in the clinic to date, there remains the potential for unintended on- and off-target effects of CRISPR nuclease activity. A variety of in silico-based prediction tools and empirically derived experimental methods have been developed to identify the most common unintended effect-small insertions and deletions at genomic sites with homology to the guide RNA. However, large-scale aberrations have recently been reported such as translocations, inversions, deletions, and even chromothripsis. These are more difficult to detect using current workflows indicating a major unmet need in the field. In this review we summarize potential sequencing-based solutions that may be able to detect these large-scale effects even at low frequencies of occurrence. In addition, many of the current clinical trials using CRISPR involve ex vivo isolation of a patient's own stem cells, modification, and re-transplantation. However, there is growing interest in direct, in vivo delivery of genome editing tools. While this strategy has the potential to address disease in cell types that are not amenable to ex vivo manipulation, in vivo editing has only one desired outcome-on-target editing in the cell type of interest. CRISPR activity in unintended cell types (both on- and off-target) is therefore a major safety as well as ethical concern in tissues that could enable germline transmission. In this review, we have summarized the strengths and weaknesses of current editing and delivery tools and potential improvements to off-target and off-tissue CRISPR activity detection. We have also outlined potential mitigation strategies that will ensure that the safety of CRISPR keeps pace with efficacy, a necessary requirement if this technology is to realize its full translational potential.
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Affiliation(s)
- Beeke Wienert
- Graphite Bio, Inc., South San Francisco, CA, United States
| | - M. Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States,Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA, United States,*Correspondence: M. Kyle Cromer,
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Hoa NPA, Lien NTK, Tung NV, Lan NN, Mai NTP, Huong NTM, Thach HN, Hoang NH. Biliary atresia combined Wilson disease identified by whole exome sequencing in Vietnamese patient with severe liver failure. Medicine (Baltimore) 2022; 101:e28547. [PMID: 35029214 PMCID: PMC8757933 DOI: 10.1097/md.0000000000028547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/22/2021] [Indexed: 01/05/2023] Open
Abstract
RATIONALE Hepatobiliary diseases such as biliary atresia (BA), Wilson disease, and progressive familial intrahepatic cholestasis are common causes of morbidity and mortality in young children. Affected patients progress rapidly to end-stage cirrhosis and require liver transplantation or die. Mutations in many genes have been identified to play an important role in the pathogenesis of hepatobiliary diseases. PATIENT CONCERNS AND DIAGNOSIS In this study, we identified mutations in an 8-year-old girl who had severe liver failure. The patient was first diagnosed with BA at 2.5 months of age and has undergone Kasai surgery to connect the umbilical cord and jejunum. After that, the patient suddenly had unusual developments with symptoms of jaundice, acute liver failure with hemolysis. She was tested and diagnosed with Wilson disease. INTERVENTIONS AND OUTCOMES She was treated according to the regimen for a patient with Wilson disease but had abnormal progress leading to severe liver failure. Genetic analysis was performed by whole exome sequencing and Sanger sequencing methods. The genetic analysis revealed that the patient had a homozygous mutation (p.Gly17Glyfs77∗) in the KRT18 gene, a double heterozygous mutation (p.Ser105∗ and p.Pro992Leu) in the ATP7B gene, and a homozygous variant (p.Val444Ala) in the ABCB11 gene. In silico prediction of mutations indicated that these mutations are the cause of the severe liver failure in the patient. LESSON This is a rare clinical case of a BA patient combined with Wilson disease. Our results suggested that whole exome sequencing is an effective diagnostic tool and emphasizes the importance of early diagnosis and appropriate management to save lives and prevent serious complications in the patient.
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Affiliation(s)
- Nguyen Pham Anh Hoa
- Hepatology Department, Vietnam National Hospital of Pediatrics, Ministry of Health, 18/879 La Thanh Str., Dongda, Hanoi, Vietnam
| | - Nguyen Thi Kim Lien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 - Hoang Quoc Viet Str., Caugiay, Hanoi, Vietnam
| | - Nguyen Van Tung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 - Hoang Quoc Viet Str., Caugiay, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Vietnam
| | - Nguyen Ngoc Lan
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 - Hoang Quoc Viet Str., Caugiay, Hanoi, Vietnam
| | - Nguyen Thi Phuong Mai
- Human Genetics Department, Vietnam National Hospital of Pediatrics, Ministry of Health, 18/879 La Thanh Str., Dongda, Hanoi, Vietnam
| | - Nguyen Thi Mai Huong
- Human Genetics Department, Vietnam National Hospital of Pediatrics, Ministry of Health, 18/879 La Thanh Str., Dongda, Hanoi, Vietnam
| | - Hoang Ngoc Thach
- Pathology Department, Vietnam National Hospital of Pediatrics, Ministry of Health, 18/879 La Thanh Str., Dongda, Hanoi, Vietnam
| | - Nguyen Huy Hoang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 - Hoang Quoc Viet Str., Caugiay, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Vietnam
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9
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Hypothalamic kisspeptin and kisspeptin receptors: Species variation in reproduction and reproductive behaviours. Front Neuroendocrinol 2022; 64:100951. [PMID: 34757093 DOI: 10.1016/j.yfrne.2021.100951] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/22/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
Abstract
Kisspeptin, encoded by the KISS1 gene, was first discovered as a potential metastasis suppressor gene. The prepro-kisspeptin precursor is cleaved into shorter mature bioactive peptides of varying sizes that bind to the G protein-coupled receptor GPR54 (=KISS1R). Over the last two decades, multiple types of Kiss and KissR genes have been discovered in mammalian and non-mammalian vertebrate species, but they are remarkably absent in birds. Kiss neuronal populations are distributed mainly in the hypothalamus. The KissRs are widely distributed in the brain, including the hypothalamic and non-hypothalamic regions, such as the hippocampus, amygdala, and habenula. The role of KISS1-KISS1R in humans and Kiss1-Kiss1R in rodents is associated with puberty, gonadal maturation, and the reproductive axis. However, recent gene deletion studies in zebrafish and medaka have provided controversial results, suggesting that the reproductive role of kiss is dispensable. This review highlights the evolutionary history, localisation, and significance of Kiss-KissR in reproduction and reproductive behaviours in mammalian and non-mammalian vertebrates.
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Sahaba SA, Rashid MA, Islam MS, Nahid NA, Apu MNH, Sultana TN, Chaity NI, Hasan MM, Islam MS. The link of ERCC2 rs13181 and ERCC4 rs2276466 polymorphisms with breast cancer in the Bangladeshi population. Mol Biol Rep 2021; 49:1847-1856. [PMID: 34837148 DOI: 10.1007/s11033-021-06994-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/19/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Breast cancer (BC) is the most common disease in women and the leading cause of death from cancer globally. Epidemiological studies examined that nucleotide excision repair genes ERCC2 (rs13181) and ERCC4 (rs2276466) SNPs might increase cancer risk. Based on the previous investigation, this study was conducted to explore the correlation between these polymorphisms and BC susceptibility in Bangladeshi women. METHODS AND RESULTS Between January 2019 and January 2020, 140 blood samples were collected from female patients histologically diagnosed with BC, and 111 female controls were recruited from non-cancer subjects. Genotyping was performed applying the PCR-RFLP method, and all statistical analyzes were conducted using SPSS, version 25.0. Comparison of characteristics and clinicopathological features between ERCC2 rs13181 and ERCC4 rs2276466 carriers and non-carriers showed no significant link with BC. Analysis of ERCC2 rs13181 with the risk of BC showed that the GG genotype and G allele carriers showed a fourfold and 1.78-fold higher risk (OR 4.00, P = 0.001 and OR 1.78, P = 0.002) that are statistically significant. In addition, the patients with combined TG+GG genotype revealed a 2.09-fold increased chance (OR 2.09, P = 0.020) BC development. Analysis of recessive model (GG vs. TT+TG) also depicted 2.74-times significantly higher risk (OR 2.74, P = 0.002). On the other hand, ERCC4 rs2276466 polymorphism did not show any significant association with BC (P > 0.05). CONCLUSIONS Our findings show that ERCC2 rs13181 is linked to an elevated risk of BC. Our study also shows that ERCC4 rs2276466 polymorphism has no substantial risk of BC in the Bangladeshi population.
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Affiliation(s)
- Shaid All Sahaba
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | | | - Md Saiful Islam
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Noor Ahmed Nahid
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Mohd Nazmul Hasan Apu
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Taposhi Nahid Sultana
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Nusrat Islam Chaity
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Md Mehedi Hasan
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Safiqul Islam
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh.
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11
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Juhari WKW, Ahmad Amin Noordin KB, Zakaria AD, Rahman WFWA, Mokhter WMMWM, Hassan MRA, Sidek ASM, Zilfalil BA. Whole-Genome Profiles of Malay Colorectal Cancer Patients with Intact MMR Proteins. Genes (Basel) 2021; 12:genes12091448. [PMID: 34573430 PMCID: PMC8471947 DOI: 10.3390/genes12091448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/12/2022] Open
Abstract
Background: This study aimed to identify new genes associated with CRC in patients with normal mismatch repair (MMR) protein expression. Method: Whole-genome sequencing (WGS) was performed in seven early-age-onset Malay CRC patients. Potential germline genetic variants, including single-nucleotide variations and insertions and deletions (indels), were prioritized using functional and predictive algorithms. Results: An average of 3.2 million single-nucleotide variations (SNVs) and over 800 indels were identified. Three potential candidate variants in three genes—IFNE, PTCH2 and SEMA3D—which were predicted to affect protein function, were identified in three Malay CRC patients. In addition, 19 candidate genes—ANKDD1B, CENPM, CLDN5, MAGEB16, MAP3K14, MOB3C, MS4A12, MUC19, OR2L8, OR51Q1, OR51AR1, PDE4DIP, PKD1L3, PRIM2, PRM3, SEC22B, TPTE, USP29 and ZNF117—harbouring nonsense variants were prioritised. These genes are suggested to play a role in cancer predisposition and to be associated with cancer risk. Pathway enrichment analysis indicated significant enrichment in the olfactory signalling pathway. Conclusion: This study provides a new spectrum of insights into the potential genes, variants and pathways associated with CRC in Malay patients.
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Affiliation(s)
- Wan Khairunnisa Wan Juhari
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | | | - Andee Dzulkarnaen Zakaria
- Department of Surgery, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (A.D.Z.); (W.M.M.W.M.M.)
| | - Wan Faiziah Wan Abdul Rahman
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
| | | | | | | | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Correspondence: ; Tel.: +60-9-7676531
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12
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Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
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Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
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13
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Kluesner MG, Lahr WS, Lonetree CL, Smeester BA, Qiu X, Slipek NJ, Claudio Vázquez PN, Pitzen SP, Pomeroy EJ, Vignes MJ, Lee SC, Bingea SP, Andrew AA, Webber BR, Moriarity BS. CRISPR-Cas9 cytidine and adenosine base editing of splice-sites mediates highly-efficient disruption of proteins in primary and immortalized cells. Nat Commun 2021; 12:2437. [PMID: 33893286 PMCID: PMC8065034 DOI: 10.1038/s41467-021-22009-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 02/24/2021] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas9 cytidine and adenosine base editors (CBEs and ABEs) can disrupt genes without introducing double-stranded breaks by inactivating splice sites (BE-splice) or by introducing premature stop (pmSTOP) codons. However, no in-depth comparison of these methods or a modular tool for designing BE-splice sgRNAs exists. To address these needs, we develop SpliceR ( http://z.umn.edu/spliceR ) to design and rank BE-splice sgRNAs for any Ensembl annotated genome, and compared disruption approaches in T cells using a screen against the TCR-CD3 MHC Class I immune synapse. Among the targeted genes, we find that targeting splice-donors is the most reliable disruption method, followed by targeting splice-acceptors, and introducing pmSTOPs. Further, the CBE BE4 is more effective for disruption than the ABE ABE7.10, however this disparity is eliminated by employing ABE8e. Collectively, we demonstrate a robust method for gene disruption, accompanied by a modular design tool that is of use to basic and translational researchers alike.
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Affiliation(s)
- Mitchell G Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Cara-Lin Lonetree
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Branden A Smeester
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Xiaohong Qiu
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Patricia N Claudio Vázquez
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Samuel P Pitzen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Madison J Vignes
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Samantha C Lee
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Samuel P Bingea
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Aneesha A Andrew
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.
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14
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Ghaffari T, Mirhosseini Motlagh N, Daraei A, Tafrihi M, Saravi M, Sabour D. Novel SCN5A variants identified in a group of Iranian Brugada syndrome patients. Funct Integr Genomics 2021; 21:331-340. [PMID: 33641026 DOI: 10.1007/s10142-021-00778-9] [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: 06/16/2020] [Revised: 01/26/2021] [Accepted: 02/14/2021] [Indexed: 10/22/2022]
Abstract
Brugada syndrome (BrS) is a rare hereditary arrhythmia syndrome that increases an individual's risk for sudden cardiac death (SCD) due to ventricular fibrillation. This disorder is regarded as a notable cause of death in individuals aged less than 40 years, responsible for up to 40% of sudden deaths in cases without structural heart disease, and is reported to be an endemic in Asian countries. Mutations in SCN5A are found in approximately 30% of patients with Brugada syndrome. This study aimed to investigate mutations in the SCN5A gene in a group of Iranian Brugada syndrome patients. Nine probands (n = 9, male, mean age = 39) diagnosed with Brugada syndrome were enrolled in this study. Exon 2 to 29 were amplified by PCR and subjected to direct sequencing. Eight in silico prediction tools were used to anticipate the effects of non-synonymous variants. Seven known polymorphisms and 2 previously reported disease-causing mutations, including H558R and G1406R, were found in the studied cases. Twenty novel variants were identified: 15 missense, 2 frameshift, 2 synonymous, and one nonsense variants. In silico tools predicted 11 non-synonymous variants to have damaging effects, whereas frameshift and nonsense variants were considered inherently pathogenic. The novel variants identified in this study, alongside previously reported mutations, are highly likely to be the cause of the Brugada syndrome phenotype observed in the patient group. Further analysis is required to understand the physiological effects caused by these variants.
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Affiliation(s)
- Taraneh Ghaffari
- Molecular and Cell Biology Research Lab2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, 47416-95447, Iran.,Department of Laboratory Science, Faculty of Paramedicine, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran.,Dermatology Research Institute, Suite 310, 8500 Blackfoot Trial SE, Calgary, Alberta, T2J 7E1, Canada
| | - Naser Mirhosseini Motlagh
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11 St, Babol, 47138-18983, Iran
| | - Abdolreza Daraei
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran
| | - Majid Tafrihi
- Molecular and Cell Biology Research Lab2, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, 47416-95447, Iran
| | - Mehrdad Saravi
- Department of Cardiology, Faculty of Medicine, Rohani Hospital, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran
| | - Davood Sabour
- Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Isar 11 St, Babol, 47138-18983, Iran. .,Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, Ganjafrooz St, Babol, 47176-47745, Iran.
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15
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Tang D, Liu H, Zhao Y, Qian D, Luo S, Patz EF, Su L, Shen S, ChristianI DC, Gao W, Wei Q. Genetic variants of BIRC3 and NRG1 in the NLRP3 inflammasome pathway are associated with non-small cell lung cancer survival. Am J Cancer Res 2020; 10:2582-2595. [PMID: 32905523 PMCID: PMC7471354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023] Open
Abstract
The nod-like receptor protein 3 (NLRP3) is one of the most characterized inflammasomes, and its genetic variation and functional dysregulation are involved in pathogenesis of several cancers. To systematically evaluate the role of NLRP3 in predicting outcomes of patients with non-small cell lung cancer (NSCLC), we performed a two-phase analysis for associations between genetic variants in NLRP3 inflammasome pathway genes and NSCLC survival by using a published genome-wide association study (GWAS) dataset from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial. We used multivariate Cox proportional hazards regression analysis with Bayesian false discovery probability (≤0.80) for multiple testing correction to evaluate associations between 20,730 single-nucleotide polymorphisms (SNPs) in 176 genes and overall survival of 1,185 NSCLC patients from the PLCO trial. We further validated the identified significant SNPs in another GWAS dataset with survival data from 984 NSCLC patients of the Harvard Lung Cancer Susceptibility (HLCS) study. The results showed that two independent SNPs in two different genes (i.e., BIRC3 rs11225211 and NRG1 rs4733124) were significantly associated with the NSCLC overall survival, with a combined hazards ratio (HR) of 0.83 [95% confidence interval (CI) = 0.74-0.93 and P = 0.0009] and 1.18 (95% CI = 1.06-1.31) and P = 0.002], respectively. However, further expression quantitative trait loci (eQTL) analysis showed no evidence for correlations between the two SNPs and mRNA expression levels of corresponding genes. These results indicated that genetic variants in the NLRP3 imflammasome pathway gene-sets might be predictors of NSCLC survival, but the molecular mechanisms underlying the observed associations warrant further investigations.
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Affiliation(s)
- Dongfang Tang
- Department of Thoracic Oncology, Huadong Hospital Affiliated to Fudan UniversityShanghai 200040, China
- Duke Cancer Institute, Duke University Medical CenterDurham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of MedicineDurham, NC 27710, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical CenterDurham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of MedicineDurham, NC 27710, USA
| | - Yuchen Zhao
- Duke Cancer Institute, Duke University Medical CenterDurham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of MedicineDurham, NC 27710, USA
| | - Danwen Qian
- Duke Cancer Institute, Duke University Medical CenterDurham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of MedicineDurham, NC 27710, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of MedicineDurham, NC 27710, USA
| | - Edward F Patz
- Duke Cancer Institute, Duke University Medical CenterDurham, NC 27710, USA
- Department of Radiology and Department of Pharmacology and Cancer Biology, Duke University Medical CenterDurham, NC 27710, USA
| | - Li Su
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public HealthBoston, MA 02115, USA
| | - Sipeng Shen
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public HealthBoston, MA 02115, USA
| | - David C ChristianI
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public HealthBoston, MA 02115, USA
- Department of Medicine, Massachusetts General HospitalBoston, MA 02114, USA
| | - Wen Gao
- Department of Thoracic Oncology, Huadong Hospital Affiliated to Fudan UniversityShanghai 200040, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical CenterDurham, NC 27710, USA
- Department of Population Health Sciences, Duke University School of MedicineDurham, NC 27710, USA
- Department of Medicine, Duke University School of MedicineDurham, NC 27710, USA
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16
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Non-synonymous polymorphisms in candidate gene associated with growth traits in Channel catfish (Ictalurus punctatus, Rafinesque, 1818). Mol Biol Rep 2019; 47:87-95. [PMID: 31576511 DOI: 10.1007/s11033-019-05110-0] [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: 05/16/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Resequencing of Myostatin, Growth Hormone, Follistatin-A-like, Insulin-like Growth Factor I (IGF-I) and Myogenin (MYOG) genes was completed to discover novel genetic variations and assess non synonymous (ns) polymorphisms (SNPs) effect on growth related traits of channel catfish. Wild and farmed animals were used as a discovering population. Resequencing lead to the identification of 59 new variants in the five analyzed genes; 66% found in introns and 34% in coding regions. From coding regions, 14 variants were synonyms and six were ns variations. A mutation rate of one in 129 bp was estimated. Four ns variations were selected for validation and association analysis. In IGF-I two ns polymorphisms, at IGF-I19 the G wild type allele was fixed in population and for IGF-I63 the C allele had a frequency of 0.972 and for mutate allele G of 0.027. In MYOG two ns SNPs were assessed. MYOG131 presented a frequency of alleles T and A, of 0.754 and 0.246, respectively and MYOG233, with a frequency of G and C of 0.775 and 0.225, respectively. Only MYOG131 (g.529T>A) was significantly associated (P < 0.04) to some growth traits. Results suggest MYOG131 g.529T>A as candidate locus for genetic enhancement of growth traits in channel catfish.
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17
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Li G, Liu B, Jiang Q, Zhang J, Xin S, Xu K. The association of two common polymorphisms in miRNAs with diabetes mellitus: A meta-analysis. Medicine (Baltimore) 2019; 98:e17414. [PMID: 31577754 PMCID: PMC6783178 DOI: 10.1097/md.0000000000017414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small noncoding single-stranded RNAs with a length of ∼21 nucleotides. Single nucleotide polymorphisms (SNPs) may affect the function of miRNAs, resulting in a variety of disorders in vivo. Recently, diabetes mellitus (DM) has become a global healthcare problem, and several studies have reported that 2 common polymorphisms (miRNA 146a rs2910164 and miRNA 27a rs895819) are related to susceptibility to diabetes. Given that no consensus had been reached regarding the association of the 2 polymorphisms with diabetes, we conducted this meta-analysis. METHODS Four databases (PubMed, EMBASE, Cochrane, and Web of Science) were searched up to January 9, 2019. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the association strength. Subgroup and sensitivity analyses were also performed. RESULTS Six studies involving 2585 cases and 2435 controls for miR146a rs2910164 and 5 studies involving 2922 cases and 2781 controls for miR27a rs895819 were ultimately analyzed in our meta-analysis. Based on pooled results, no statistical significance in association between rs2910164 and diabetes in Caucasians, Asians, or type 2 diabetes was observed in any genetic models. Nevertheless, we found a significant correlation between miRNA27a rs895819 and diabetes in the homozygote model (CC vs TT: OR = 0.58, 95%CI [0.35,0.98]) and recessive model (CC vs CT + TT: OR = 0.59, 95%CI [0.36,0.97]). By performing subgroup analysis, we also observed that C allele conveyed a significant protective effect against diabetes development in Caucasians (C vs T: OR = 0.67, 95%CI [0.52,0.85]). CONCLUSION In conclusion, this meta-analysis indicated that miRNA27a rs895819 might play a protective role in diabetes, and miRNA146a rs2910164 likely had no association with diabetes.
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Rajkumar MS, Garg R, Jain M. Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance. Sci Rep 2018; 8:16795. [PMID: 30429540 PMCID: PMC6235875 DOI: 10.1038/s41598-018-35140-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 10/31/2018] [Indexed: 12/16/2022] Open
Abstract
Seed size/weight is a major agronomic trait which determine crop productivity in legumes. To understand the genetic basis of seed size determination, we sought to identify DNA polymorphisms between two small (Himchana 1 and Pusa 362) and two large-seeded (JGK 3 and PG 0515) chickpea cultivars via whole genome resequencing. We identified a total of 75535 single nucleotide polymorphisms (SNPs), 6486 insertions and deletions (InDels), 1938 multi-nucleotide polymorphisms (MNPs) and 5025 complex variants between the two small and two large-seeded chickpea cultivars. Our analysis revealed 814, 244 and 72 seed-specific genes harboring DNA polymorphisms in promoter or non-synonymous and large-effect DNA polymorphisms, respectively. Gene ontology analysis revealed enrichment of cell growth and division related terms in these genes. Among them, at least 22 genes associated with quantitative trait loci, and those involved in cell growth and division and encoding transcription factors harbored promoter and/or large-effect/non-synonymous DNA polymorphisms. These also showed higher expression at late-embryogenesis and/or mid-maturation stages of seed development in the large-seeded cultivar, suggesting their role in seed size/weight determination in chickpea. Altogether, this study provided a valuable resource for large-scale genotyping applications and a few putative candidate genes that might play crucial role in governing seed size/weight in chickpea.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India. .,National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Line-1: Implications in the etiology of cancer, clinical applications, and pharmacologic targets. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 778:51-60. [DOI: 10.1016/j.mrrev.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/21/2022]
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20
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Liu C, Moschou PN. Phenotypic novelty by CRISPR in plants. Dev Biol 2018; 435:170-175. [DOI: 10.1016/j.ydbio.2018.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/21/2018] [Accepted: 01/23/2018] [Indexed: 01/15/2023]
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Mackeh R, Marr AK, Dargham SR, Syed N, Fakhro KA, Kino T. Single-Nucleotide Variations of the Human Nuclear Hormone Receptor Genes in 60,000 Individuals. J Endocr Soc 2018; 2:77-90. [PMID: 29379896 PMCID: PMC5779106 DOI: 10.1210/js.2017-00406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/28/2017] [Indexed: 01/15/2023] Open
Abstract
Nuclear hormone receptors (NRs) mediate biologic actions of lipophilic molecules to gene transcription and are phylogenetically and functionally categorized into seven subfamilies and three groups, respectively. Single-nucleotide variations (SNVs) or polymorphisms are genetic changes influencing individual response to environmental factors and susceptibility to various disorders, and are part of the genetic diversification and basis for evolution. We sorted out SNVs of the human NR genes from 60,706 individuals, calculated three parameters (percentage of all variants, percentage of loss-of-function variants, and ratio of nonsynonymous/synonymous variants in their full protein-coding or major domain-coding sequences), and compared them with several valuables. Comparison of these parameters between NRs and control groups identified that NRs form a highly conserved gene family. The three parameters for the full coding sequence are positively correlated with each other, whereas four NR genes are distinct from the others with much higher tolerance to protein sequence-changing variants. DNA-binding domain and N-terminal domain are respectively those bearing the least and the most variation. NR subfamilies based on their phylogenetic proximity or functionality as well as diversity of tissue distribution and numbers of partner molecules are all not correlated with the variation parameters, whereas their gene age demonstrates an association. Our results suggest that the natural selection driving the NR family evolution still operates in humans. Gene age and probably the potential to adapt to various new ligands, but not current functional diversity, are major determinants for SNVs of the human NR genes.
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Affiliation(s)
- Rafah Mackeh
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Alexandra K. Marr
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Soha R. Dargham
- Biostatistics, Epidemiology and Biomathematics Research Core, Weill Cornell Medicine in Qatar, Doha 24811, Qatar
| | - Najeeb Syed
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Khalid A. Fakhro
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha 24144, Qatar
| | - Tomoshige Kino
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
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Hsu MK, Lin HY, Chen FC. NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events. PLoS One 2017; 12:e0174798. [PMID: 28369084 PMCID: PMC5378362 DOI: 10.1371/journal.pone.0174798] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/15/2017] [Indexed: 01/23/2023] Open
Abstract
Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation–an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.
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Affiliation(s)
- Min-Kung Hsu
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan
| | - Hsuan-Yu Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan
| | - Feng-Chi Chen
- Department of Biological Science and Technology, National Chiao-Tung University, Hsinchu City, Taiwan
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Township, Miaoli County, Taiwan
- School of Dentistry, China Medical University, Taichung City, Taiwan
- * E-mail:
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23
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Moszyńska A, Gebert M, Collawn JF, Bartoszewski R. SNPs in microRNA target sites and their potential role in human disease. Open Biol 2017; 7:170019. [PMID: 28381629 PMCID: PMC5413909 DOI: 10.1098/rsob.170019] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/08/2017] [Indexed: 12/14/2022] Open
Abstract
In the post-genomic era, the goal of personalized medicine is to determine the correlation between genotype and phenotype. Developing high-throughput genotyping technologies such as genome-wide association studies (GWAS) and the 1000 Genomes Project (http://www.internationalgenome.org/about/#1000G_PROJECT) has dramatically enhanced our ability to map where changes in the genome occur on a population level by identifying millions of single nucleotide polymorphisms (SNPs). Polymorphisms, particularly those within the coding regions of proteins and at splice junctions, have received the most attention, but it is also now clear that polymorphisms in the non-coding regions are important. In these non-coding regions, the enhancer and promoter regions have received the most attention, whereas the 3'-UTR regions have until recently been overlooked. In this review, we examine how SNPs affect microRNA-binding sites in these regions, and how mRNA stability changes can lead to disease pathogenesis.
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Affiliation(s)
- Adrianna Moszyńska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gebert
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
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Abouelhoda M, Faquih T, El-Kalioby M, Alkuraya FS. Revisiting the morbid genome of Mendelian disorders. Genome Biol 2016; 17:235. [PMID: 27884173 PMCID: PMC5123336 DOI: 10.1186/s13059-016-1102-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/08/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign "disease mutations" are difficult to analyze due to their rarity. The Saudi Arabian variome is enriched for homozygosity due to inbreeding, a key advantage that can be exploited for the critical examination of previously published variants. RESULTS We collated all "disease-related mutations" listed in the Human Gene Mutation Database (HGMD) and ClinVar, including "variants of uncertain significance" (VOUS). We find that the use of public databases including 1000 Genomes, ExAC, and Kaviar can reclassify many of these variants as likely benign. Our Saudi Human Genome Program (SHGP) can reclassify many variants that are rare in public databases. Furthermore, SGPD allows us to observe many previously reported variants in the homozygous state and our extensive phenotyping of participants makes it possible to demonstrate the lack of phenotype for these variants, thus challenging their pathogenicity despite their rarity. We also find that 18 VOUS BRCA1 and BRCA2 variants that are listed in BRCA Exchange are present at least once in the homozygous state in patients who lack features of Fanconi anemia. Reassuringly, we could reciprocally demonstrate that none of those labeled as "pathogenic" were observed in the homozygous statue in individuals who lack Fanconi phenotype in our database. CONCLUSION Our study shows the importance of revisiting disease-related databases using public resources as well as of population-specific resources to improve the specificity of the morbid genome of Mendelian diseases in humans.
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Affiliation(s)
- Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia.
| | - Tariq Faquih
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Mohamed El-Kalioby
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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25
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Liu T, Lin K. The distribution pattern of genetic variation in the transcript isoforms of the alternatively spliced protein-coding genes in the human genome. MOLECULAR BIOSYSTEMS 2016; 11:1378-88. [PMID: 25820936 DOI: 10.1039/c5mb00132c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
By enabling the transcription of multiple isoforms from the same gene locus, alternative-splicing mechanisms greatly expand the diversity of the human transcriptome and proteome. Currently, the alternatively spliced transcripts from each protein-coding gene locus in the human genome can be classified as either principal or non-principal isoforms, providing that they differ with respect to cross-species conservation or biological features. By mapping the variants from the 1000 Genomes Project onto the coding region of each isoform, an interesting pattern of the genetic variation distributions of the coding regions for these two types of transcript isoforms was revealed on a whole-genome scale: compared with the principal isoform-specific coding regions, the non-principal isoform-specific coding regions are significantly enriched in amino acid-changing variants, particularly those that have a strong impact on protein function and have higher derived allele frequencies, suggesting that non-principal isoform-specific substitutions are less likely to be related to phenotype changes or disease. The results herein can help us better understand the potential consequences of alternatively spliced products from a population perspective.
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Affiliation(s)
- Ting Liu
- College of Life Sciences, Beijing Normal University, No. 19, Xinjiekouwai Street, Haidian District, Beijing, 100875, P. R. China.
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26
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Seo S, Takayama K, Uno K, Ohi K, Hashimoto R, Nishizawa D, Ikeda K, Ozaki N, Nabeshima T, Miyamoto Y, Nitta A. Functional analysis of deep intronic SNP rs13438494 in intron 24 of PCLO gene. PLoS One 2013; 8:e76960. [PMID: 24167553 PMCID: PMC3805565 DOI: 10.1371/journal.pone.0076960] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/29/2013] [Indexed: 11/28/2022] Open
Abstract
The single nucleotide polymorphism (SNP) rs13438494 in intron 24 of PCLO was significantly associated with bipolar disorder in a meta-analysis of genome-wide association studies. In this study, we performed functional minigene analysis and bioinformatics prediction of splicing regulatory sequences to characterize the deep intronic SNP rs13438494. We constructed minigenes with A and C alleles containing exon 24, intron 24, and exon 25 of PCLO to assess the genetic effect of rs13438494 on splicing. We found that the C allele of rs13438494 reduces the splicing efficiency of the PCLO minigene. In addition, prediction analysis of enhancer/silencer motifs using the Human Splice Finder web tool indicated that rs13438494 induces the abrogation or creation of such binding sites. Our results indicate that rs13438494 alters splicing efficiency by creating or disrupting a splicing motif, which functions by binding of splicing regulatory proteins, and may ultimately result in bipolar disorder in affected people.
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Affiliation(s)
- Seunghee Seo
- Department of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
- Department of Pharmaceutical Education, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Kanako Takayama
- Department of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Kyosuke Uno
- Department of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Kazutaka Ohi
- Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ryota Hashimoto
- Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
- Molecular Research Center for Children’s Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan
| | - Daisuke Nishizawa
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kazutaka Ikeda
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Norio Ozaki
- Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Toshitaka Nabeshima
- Department of Regional Pharmaceutical Care and Science, Meijo University, Nagoya, Japan
| | - Yoshiaki Miyamoto
- Department of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Atsumi Nitta
- Department of Pharmaceutical Therapy and Neuropharmacology, Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
- * E-mail:
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27
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RNA-Seq approach for genetic improvement of meat quality in pig and evolutionary insight into the substrate specificity of animal carbonyl reductases. PLoS One 2012; 7:e42198. [PMID: 22962580 PMCID: PMC3433470 DOI: 10.1371/journal.pone.0042198] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 07/05/2012] [Indexed: 11/19/2022] Open
Abstract
Changes in meat quality traits are strongly associated with alterations in postmortem metabolism which depend on genetic variations, especially nonsynonymous single nucleotide variations (nsSNVs) having critical effects on protein structure and function. To selectively identify metabolism-related nsSNVs, next-generation transcriptome sequencing (RNA-Seq) was carried out using RNAs from porcine liver, which contains a diverse range of metabolic enzymes. The multiplex SNV genotyping analysis showed that various metabolism-related genes had different nsSNV alleles. Moreover, many nsSNVs were significantly associated with multiple meat quality traits. Particularly, ch7:g.22112616A>G SNV was identified to create a single amino acid change (Thr/Ala) at the 145th residue of H1.3-like protein, very close to the putative 147th threonine phosphorylation site, suggesting that the nsSNV may affect multiple meat quality traits by affecting the epigenetic regulation of postmortem metabolism-related gene expression. Besides, one nonsynonymous variation, probably generated by gene duplication, led to a stop signal in porcine testicular carbonyl reductase (PTCR), resulting in a C-terminal (E281-A288) deletion. Molecular docking and energy minimization calculations indicated that the binding affinity of wild-type PTCR to 5α-DHT, a C21-steroid, was superior to that of C-terminal-deleted PTCR or human carbonyl reductase, which was very consistent with experimental data, reported previously. Furthermore, P284 was identified as an important residue mediating the specific interaction between PTCR and 5α-DHT, and phylogenetic analysis showed that P284 is an evolutionarily conserved residue among animal carbonyl reductases, which suggests that the C-terminal tails of these reductases may have evolved under evolutionary pressure to increase the substrate specificity for C21-steroids and facilitate metabolic adaptation. Altogether, our RNA-Seq revealed that selective nsSNVs were associated with meat quality traits that could be useful for successful marker-assisted selection in pigs and also represents a useful resource to enhance understanding of protein folding, substrate specificity, and the evolution of enzymes such as carbonyl reductase.
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Savas S, Geraci J, Jurisica I, Liu G. A comprehensive catalogue of functional genetic variations in the EGFR pathway: protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research. Int J Cancer 2009; 125:1257-65. [PMID: 19499547 DOI: 10.1002/ijc.24535] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The EGFR pathway is a critical signaling pathway deregulated in many solid tumors. In addition to the initiation and progression of cancer, the EGFR pathway is also implicated in variable treatment responses and prognoses. Genetic variation in the form of Single Nucleotide Polymorphisms (SNPs) can affect the function/expression of the EGFR pathway genes. Here, we applied a systematic and comprehensive approach utilizing diverse public databases and in silico analysis tools to select putative functional genetic variations from 244 genes involved in the EGFR pathway. Our data comprises 649 SNPs. Three hundred sixty SNPs are predicted to have biological consequences (functional SNPs). These SNPs can be directly used in further studies to test their association with risk, treatment response and prognosis in cancer. To systematically cover the EGFR pathway, we also performed a network-based analysis to further select putative functional SNPs from the genes whose protein products physically interact with the EGFR pathway proteins. We utilized protein-protein interaction information and focused on 14 proteins that have a high degree of connectivity (interacting with > or = 10 proteins) with the EGFR pathway genes identified to have functional SNPs (f-EGFR genes). Two of these proteins (FYN and LCK) had interactions with 17 of the f-EGFR genes, yet both lacked any putative functional SNP. However, our analysis indicated the presence of potentially functional SNPs in 9 other highly interactive proteins. The genes and their SNPs identified in the network-based analysis represent potential candidates for gene-gene and SNP-SNP interaction studies in cancer research.
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Affiliation(s)
- Sevtap Savas
- Division of Applied Molecular Oncology, Department of Medical Biophysics, Ontario Cancer Institute, Toronto, Ontario, Canada.
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Abstract
Rare, high-penetrance genetic variations account for a small portion of genetic cancer syndromes. In contrast, most cancers develop from a combination of minor genetic influences and environmental factors. There are numerous publications on cancer susceptibility. In contrast, genetic studies in treatment response and outcome analyses are a rapidly emerging field. Approaches used in disease susceptibility can be adapted for genetic outcome studies. In this review, we summarize the current knowledge on how candidate genes and genetic variations are selected to evaluate gene-outcome, gene-prognosis, and gene-treatment response relationships as applicable to the practicing oncologist.
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Affiliation(s)
- Sevtap Savas
- Division of Applied Molecular Oncology, Department of Medical Biophysics, Ontario Cancer Institute, Toronto, Canada.
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Hasin-Brumshtein Y, Lancet D, Olender T. Human olfaction: from genomic variation to phenotypic diversity. Trends Genet 2009; 25:178-84. [PMID: 19303166 DOI: 10.1016/j.tig.2009.02.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/06/2009] [Accepted: 02/06/2009] [Indexed: 12/19/2022]
Abstract
The sense of smell is a complex molecular device, encompassing several hundred olfactory receptor proteins (ORs). These receptors, encoded by the largest human gene superfamily, integrate odorant signals into an accurate 'odor image' in the brain. Widespread phenotypic diversity in human olfaction is, in part, attributable to prevalent genetic variation in OR genes, owing to copy number variation, deletion alleles and deleterious single nucleotide polymorphisms. The development of new genomic tools, including next generation sequencing and CNV assays, provides opportunities to characterize the genetic variations of this system. The advent of large-scale functional screens of expressed ORs, combined with genetic association studies, has the potential to link variations in ORs to human chemosensory phenotypes. This promises to provide a genome-wide view of human olfaction, resulting in a deeper understanding of personalized odor coding, with the potential to decipher flavor and fragrance preferences.
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Affiliation(s)
- Yehudit Hasin-Brumshtein
- Department of Molecular Genetics and the Crown Human Genome Center, Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Yngvadottir B, Xue Y, Searle S, Hunt S, Delgado M, Morrison J, Whittaker P, Deloukas P, Tyler-Smith C. A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs. Am J Hum Genet 2009; 84:224-34. [PMID: 19200524 DOI: 10.1016/j.ajhg.2009.01.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 01/10/2009] [Accepted: 01/14/2009] [Indexed: 12/17/2022] Open
Abstract
Nonsense SNPs introduce premature termination codons into genes and can result in the absence of a gene product or in a truncated and potentially harmful protein, so they are often considered disadvantageous and are associated with disease susceptibility. As such, we might expect the disrupted allele to be rare and, in healthy people, observed only in a heterozygous state. However, some, like those in the CASP12 and ACTN3 genes, are known to be present at high frequencies and to occur often in a homozygous state and seem to have been advantageous in recent human evolution. To evaluate the selective forces acting on nonsense SNPs as a class, we have carried out a large-scale experimental survey of nonsense SNPs in the human genome by genotyping 805 of them (plus control synonymous SNPs) in 1,151 individuals from 56 worldwide populations. We identified 169 genes containing nonsense SNPs that were variable in our samples, of which 99 were found with both copies inactivated in at least one individual. We found that the sampled humans differ on average by 24 genes (out of about 20,000) because of these nonsense SNPs alone. As might be expected, nonsense SNPs as a class were found to be slightly disadvantageous over evolutionary timescales, but a few nevertheless showed signs of being possibly advantageous, as indicated by unusually high levels of population differentiation, long haplotypes, and/or high frequencies of derived alleles. This study underlines the extent of variation in gene content within humans and emphasizes the importance of understanding this type of variation.
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32
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Genome-wide survey of allele-specific splicing in humans. BMC Genomics 2008; 9:265. [PMID: 18518984 PMCID: PMC2427040 DOI: 10.1186/1471-2164-9-265] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 06/02/2008] [Indexed: 12/31/2022] Open
Abstract
Background Accurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence. Many examples of mutations within human splice regulatory regions that alter splicing qualitatively or quantitatively have been reported and allelic differences in mRNA splicing are likely to be a common and important source of phenotypic diversity at the molecular level, in addition to their contribution to genetic disease susceptibility. However, because the effect of a mutation on the efficiency of mRNA splicing is often difficult to predict, many mutations that cause disease through an effect on splicing are likely to remain undiscovered. Results We have combined a genome-wide scan for sequence polymorphisms likely to affect mRNA splicing with analysis of publicly available Expressed Sequence Tag (EST) and exon array data. The genome-wide scan uses published tools and identified 30,977 SNPs located within donor and acceptor splice sites, branch points and exonic splicing enhancer elements. For 1,185 candidate splicing polymorphisms the difference in splicing between alternative alleles was corroborated by publicly available exon array data from 166 lymphoblastoid cell lines. We developed a novel probabilistic method to infer allele-specific splicing from EST data. The method uses SNPs and alternative mRNA isoforms mapped to EST sequences and models both regulated alternative splicing as well as allele-specific splicing. We have also estimated heritability of splicing and report that a greater proportion of genes show evidence of splicing heritability than show heritability of overall gene expression level. Our results provide an extensive resource that can be used to assess the possible effect on splicing of human polymorphisms in putative splice-regulatory sites. Conclusion We report a set of genes showing evidence of allele-specific splicing from an integrated analysis of genomic polymorphisms, EST data and exon array data, including several examples for which there is experimental evidence of polymorphisms affecting splicing in the literature. We also present a set of novel allele-specific splicing candidates and discuss the strengths and weaknesses of alternative technologies for inferring the effect of sequence variants on mRNA splicing.
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33
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Schuster-Böckler B, Bateman A. Protein interactions in human genetic diseases. Genome Biol 2008; 9:R9. [PMID: 18199329 PMCID: PMC2395246 DOI: 10.1186/gb-2008-9-1-r9] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 11/27/2007] [Accepted: 01/16/2008] [Indexed: 11/10/2022] Open
Abstract
A method is presented to identify residues that form part of an interaction interface, leading to the prediction that 1,428 OMIM mutations are related to an interaction defect. We present a novel method that combines protein structure information with protein interaction data to identify residues that form part of an interaction interface. Our prediction method can retrieve interaction hotspots with an accuracy of 60% (at a 20% false positive rate). The method was applied to all mutations in the Online Mendelian Inheritance in Man (OMIM) database, predicting 1,428 mutations to be related to an interaction defect. Combining predicted and hand-curated sets, we discuss how mutations affect protein interactions in general.
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Han A, Kim WY, Park SM. SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay. Bioinformatics 2006; 23:397-9. [PMID: 17121775 DOI: 10.1093/bioinformatics/btl593] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED Elucidating the effects of genetic polymorphisms on genes and gene networks is an important step in disease association studies. We developed the SNP2NMD database for human SNPs (single nucleotide polymorphisms) that result in PTCs (premature termination codons) and trigger nonsense-mediated mRNA decay (NMD). The SNP2NMD Web interfaces provide extensive genetic information on and graphical views of the queried SNP, gene, and disease terms. AVAILABILITY SNP2NMD is available from http://variome.net, or directly from http://bioportal.kobic.re.kr/SNP2NMD. SUPPLEMENTARY INFORMATION http://bioportal.kobic.re.kr/SNP2NMD/Wiki.jsp?page=Statistics.
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Affiliation(s)
- Areum Han
- Korean Bioinformation Center, KRIBB, Daejeon 305-806, Korea
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