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Pang R, Li S, Chen W, Yuan L, Xiao H, Xing K, Li Y, Zhang Z, He X, Zhang W. Insecticide resistance reduces the profitability of insect-resistant rice cultivars. J Adv Res 2024; 60:1-12. [PMID: 37499938 PMCID: PMC11156607 DOI: 10.1016/j.jare.2023.07.009] [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: 05/13/2023] [Revised: 07/02/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
INTRODUCTION Preventing crop yield loss caused by pests is critical for global agricultural production. Agricultural pest control has largely relied on chemical pesticides. The interaction between insecticide resistance and the adaptation of herbivorous pests to host plants may represent an emerging threat to future food security. OBJECTIVES This study aims to unveil genetic evidence for the reduction in the profitability of resistant cultivars derived from insecticide resistance in target pest insects. METHODS An experimental evolution system encompassing resistant rice and its major monophagous pest, the brown planthopper Nilaparvata lugens, was constructed. Whole genome resequencing and selective sweep analysis were utilized to identify the candidate gene loci related to the adaptation. RNA interference and induced expression assay were conducted to validate the function of the candidate loci. RESULTS We found that the imidacloprid-resistant population of N. lugens rapidly adapted to resistant rice IR36. Gene loci related to imidacloprid resistance may contribute to this phenomenon. Multiple alleles in the nicotinic acetylcholine receptor (nAChR)-7-like and P450 CYP4C61 were significantly correlated with changes in virulence to IR36 rice and insecticide resistance of N. lugens. One avirulent/susceptible genotype and two virulent/resistant genotypes could be inferred from the corresponding alleles. Importantly, we found that the virulent/resistant genotypes already exist in the wild in China, exhibiting increasing frequencies along with insecticide usage. We validated the relevance of these genotypes and the virulence to three more resistant rice cultivars. Knockdown of the above two genes in N. lugens significantly decreased both the resistance to imidacloprid and the virulence towards resistant rice. CONCLUSION Our findings provide direct genetic evidence to the eco-evolutionary consequence of insecticide resistance, and suggest an urgent need for the implementation of predictably sustainable pest management.
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Affiliation(s)
- Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China; National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shihui Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weiwen Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Longyu Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Hanxiang Xiao
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Ke Xing
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanfang Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhenfei Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
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Miao M, Wang J, Guo C, Su X, Sun L, Lu S. Identification of a novel de novo PUF60 variant causing Verheij syndrome in a fetus. Gene 2024; 897:148092. [PMID: 38110042 DOI: 10.1016/j.gene.2023.148092] [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: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Verheij syndrome (VRJS) is a craniofacial spliceosomopathy with a wide phenotypic spectrum. Haploinsufficiency of the poly-uridine binding splicing factor 60 gene (PUF60) and its loss-of-function (LOF) variants are involved in VRJS. We evaluated a human fetus with congenital heart defects and preaxial polydactyly. Clinical data were obtained from the medical record. Whole-exome sequencing (WES) was used to explore the potential genetic etiology, and the detected variant verified using Sanger sequencing. Functional studies were performed to validate the pathogenic effects of the variant. Using trio-WES, we identified a novel PUF60 variant (NM_078480.2; c.1678 T > A, p.*560Argext*204) in the pedigree. Bioinformatic analyses revealed that the variant is potentially pathogenic, and functional studies indicated that it leads to degradation of the elongated protein and subsequently PUF60 LOF, producing some VRJS phenotypes. These findings confirmed the pathogenicity of the variant. This study implicates PUF60 LOF in the etiopathogenesis of VRJS. It not only expands the PUF60 variant spectrum, and also provides a basis for genetic counseling and the diagnosis of VRJS. Although trio-WES is a well-established approach for identifying the genetic etiology of rare multisystemic conditions, functional studies could aid in verifying the pathogenicity of novel variants.
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Affiliation(s)
- Mingzhu Miao
- Department of Prenatal Diagnosis, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China
| | - Jue Wang
- Department of Prenatal Diagnosis, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China
| | - Chenyan Guo
- Department of Obstetrics, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China
| | - Xiaotian Su
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Lizhou Sun
- Department of Obstetrics, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China.
| | - Shoulian Lu
- Department of Prenatal Diagnosis, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China.
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3
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Al-Shuhaib MBS, Hashim HO. Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis. J Genet Eng Biotechnol 2023; 21:115. [PMID: 37955813 PMCID: PMC10643650 DOI: 10.1186/s43141-023-00587-6] [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: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Sanger dideoxy sequencing is vital in clinical analysis due to its accuracy, ability to analyze genetic markers like SNPs and STRs, capability to generate reliable DNA profiles, and its role in resolving complex clinical cases. The precision and robustness of Sanger sequencing contribute significantly to the scientific basis of clinical investigations. Though the reading of chromatograms seems to be a routine step, many errors conducted in PCR may lead to consequent limitations in the readings of AGCT peaks. These errors are possibly associated with improper DNA amplification and its subsequent interpretation of DNA sequencing files, such as noisy peaks, artifacts, and confusion between double-peak technical errors, heterozygosity, and double infection potentials. Thus, it is not feasible to read nucleic acid sequences without giving serious attention to these technical problems. To ensure the accuracy of DNA sequencing outcomes, it is also imperative to detect and rectify technical challenges that may lead to misinterpretation of the DNA sequence, resulting in errors and incongruities in subsequent analyses. SHORT CONCLUSION This overview sheds light on prominent technical concerns that can emerge prior to and during the interpretation of DNA chromatograms in Sanger sequencing, along with offering strategies to address them effectively. The significance of identifying and tackling these technical limitations during the chromatogram analysis is underscored in this review. Recognizing these concerns can aid in enhancing the quality of downstream analyses for Sanger sequencing results, which holds notable improvement in accuracy, reliability, and ability to provide crucial genetic information in clinical analysis.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim 8, Babil, 51001, Iraq.
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, 51001, Iraq
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Miao M, Feng L, Wang J, Xu C, Su X, Zhang G, Lu S. A novel PKHD1 splicing variant identified in a fetus with autosomal recessive polycystic kidney disease. Front Genet 2023; 14:1207772. [PMID: 37456659 PMCID: PMC10339289 DOI: 10.3389/fgene.2023.1207772] [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: 04/18/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Objective: Variants of the polycystic kidney and hepatic disease 1 (PKHD1) gene are associated with autosomal recessive polycystic kidney disease (ARPKD). This study aimed to identify the genetic causes in a Chinese pedigree with ARPKD and design a minigene construct of the PKHD1 gene to investigate the impact of its variants on splicing. Methods: Umbilical cord samples from the proband and peripheral blood samples from his parents were collected, and genomic DNA was extracted for whole-exome sequencing (WES). Bioinformatic analysis was used to identify potential genetic causes, and Sanger sequencing confirmed the existence of variants within the pedigree. A minigene assay was performed to validate the effects of an intronic variant on mRNA splicing. Results: Two variants, c.9455del (p.N3152Tfs*10) and c.2408-13C>G, were identified in the PKHD1 gene (NM_138694.4) by WES; the latter has not been previously reported. In silico analysis predicted that this intronic variant is potentially pathogenic. Bioinformatic splice prediction tools revealed that the variant is likely to strongly impact splice site function. An in vitro minigene assay revealed that c.2408-13C>G can cause aberrant splicing, resulting in the retention of 12 bp of intron 23. Conclusion: A novel pathogenic variant of PKHD1, c.2408-13C>G, was found in a fetus with ARPKD, which enriches the variant spectrum of the PKHD1 gene and provides a basis for genetic counseling and the diagnosis of ARPKD. Minigenes are optimal to determine whether intron variants can cause aberrant splicing.
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Affiliation(s)
- Mingzhu Miao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liqun Feng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jue Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cheng Xu
- Department of Pathology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaotian Su
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Guoying Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shoulian Lu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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5
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Miao M, Lu S, Sun X, Zhao M, Wang J, Su X, Jin B, Sun L. Identification of a novel heterozygous missense TP63 variant in a Chinese pedigree with split-hand/foot malformation. BMC Med Genomics 2022; 15:157. [PMID: 35831859 PMCID: PMC9281006 DOI: 10.1186/s12920-022-01311-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tumor protein p63 is an important transcription factor regulating epithelial morphogenesis. Variants associated with the TP63 gene are known to cause multiple disorders. In this study, we determined the genetic cause of split-hand/foot malformation in a Chinese pedigree. METHODS For this study, we have recruited a Chinese family and collected samples from affected and normal individuals of the family (three affected and two normal). Whole exome sequencing was performed to detect the underlying genetic defect in this family. The potential variant was validated using the Sanger sequencing approach. RESULTS Using whole-exome and Sanger sequencing, we identified a novel heterozygous pathogenic missense variant in TP63 (NM_003722.5: c.921G > T; p.Met307Ile). This variant resulted in the substitution of methionine with isoleucine. Structural analysis suggested a resulting change in the structure of a key functional domain of the p63 protein. CONCLUSION This novel missense variant expands the TP63 variant spectrum and provides a basis for genetic counseling and prenatal diagnosis of families with split-hand/foot malformation or other TP63-related diseases.
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Affiliation(s)
- Mingzhu Miao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Shoulian Lu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Xiao Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Meng Zhao
- Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Jue Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Xiaotan Su
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Bai Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
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6
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Reconstruction of evolving gene variants and fitness from short sequencing reads. Nat Chem Biol 2021; 17:1188-1198. [PMID: 34635842 PMCID: PMC8551035 DOI: 10.1038/s41589-021-00876-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
Directed evolution can generate proteins with tailor-made activities. However, full-length genotypes, their frequencies and fitnesses are difficult to measure for evolving gene-length biomolecules using most high-throughput DNA sequencing methods, as short read lengths can lose mutation linkages in haplotypes. Here we present Evoracle, a machine learning method that accurately reconstructs full-length genotypes (R2 = 0.94) and fitness using short-read data from directed evolution experiments, with substantial improvements over related methods. We validate Evoracle on phage-assisted continuous evolution (PACE) and phage-assisted non-continuous evolution (PANCE) of adenine base editors and OrthoRep evolution of drug-resistant enzymes. Evoracle retains strong performance (R2 = 0.86) on data with complete linkage loss between neighboring nucleotides and large measurement noise, such as pooled Sanger sequencing data (~US$10 per timepoint), and broadens the accessibility of training machine learning models on gene variant fitnesses. Evoracle can also identify high-fitness variants, including low-frequency 'rising stars', well before they are identifiable from consensus mutations.
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7
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Wu L, Zhang W, Li Y, Zhou D, Zhang B, Xu A, Wu Z, Wu L, Li S, Wang X, Zhao X, Wang Q, Li M, Wang Y, You H, Huang J, Ou X, Jia J. Correlation of genotype and phenotype in 32 patients with hereditary hemochromatosis in China. Orphanet J Rare Dis 2021; 16:398. [PMID: 34583728 PMCID: PMC8479922 DOI: 10.1186/s13023-021-02020-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 09/20/2021] [Indexed: 12/22/2022] Open
Abstract
Background Hereditary hemochromatosis (HH) is widely recognized and clinical manifestations of hemochromatosis-related (HFE-related) HH is well studied in European populations. Less is known about the clinical and laboratory characteristics of non-HFE related HH in Asian population. We aimed to explore the relationship between genotype and clinical phenotype in Chinese patients with non-HFE related hereditary hemochromatosis. Methods Peripheral blood samples and clinical data of patients with primary iron overload were collected from the China Registry of Genetic/Metabolic Liver Diseases. Sanger sequencing was performed in cases with primary iron overload, for 5 known HH related genes (HFE, HJV, HAMP, TFR2 and SLC40A1) and 2 novel iron homeostasis-related genes (DENND3 and SUGP2). The correlation of genotype and clinical phenotype in these patients was analyzed. Results Of the 32 patients with primary iron overload (23 were males and 9 were females), non-HFE variants were detected in 31 (31/32, 97%), including 8 pathogenic variants in HJV, 7 pathogenic variants in SLC40A1, 8 likely pathogenic variants in SUGP2 and 5 likely pathogenic variants in DENND3 cases. Among these 31 cases, 4 cases harbored homozygous variants, 2 cases harbored homozygous + heterozygous variants, 19 cases harbored heterozygous or combined heterozygous variants, and 6 cases harbored no any damaging variants. None of investigated cases carried damaging HAMP and TFR2 variants were found. 8 cases were classified as type 2A HH and 6 cases as type 4 HH, 10 cases as non-classical genotype, and 6 cases had no pathogenic variants from 31 cases. During the statistical analysis, we excluded one case (SLC40A1 IVS3 + 10delGTT + SUGP2 p. R639Q(homo)) with difficulty in grouping due to combined damaging variants. Cases with type 2A HH have an earlier age at diagnosis (p = 0.007). The iron index of cases in type 2A HH and type 4 HH was higher than that in other groups (p = 0.01). Arthropathy was relatively rare in all groups. None of cases with type 2A HH developed cirrhosis. Cirrhosis and diabetes are more prevalent in type 4 HH. The incidence of cirrhosis (p = 0.011), cardiac involvement (p = 0.042), diabetes (p = 0.035) and hypogonadism (p = 0.020) was statistically significant in the four groups. However, due to the limited sample size, the pairwise comparison showed no significant difference. Conclusions This is the first comprehensive analysis about the gene variant spectrum and phenotypic aspects of non-HFE HH in China. The results will be useful to the identification, diagnosis and management of HH in China.
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Affiliation(s)
- Liyan Wu
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Wei Zhang
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Yanmeng Li
- National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.,Liver Research Center, Experimental Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China
| | - Donghu Zhou
- National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.,Liver Research Center, Experimental Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China
| | - Bei Zhang
- National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.,Liver Research Center, Experimental Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China
| | - Anjian Xu
- National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.,Liver Research Center, Experimental Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China
| | - Zhen Wu
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Lina Wu
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Shuxiang Li
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Xiaoming Wang
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Xinyan Zhao
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Qianyi Wang
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Min Li
- Department of Clinical Epidemiology and EBM, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Yu Wang
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Hong You
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China
| | - Jian Huang
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China. .,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China. .,Liver Research Center, Experimental Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China.
| | - Xiaojuan Ou
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China. .,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.
| | - Jidong Jia
- Beijing Key Laboratory of Translational Medicine On Liver Cirrhosis , Liver Research Center, Beijing Friendship Hospital, Capital Medical University, 95 Yong-An Road, Beijing, 100050, China. .,National Clinical Research Center for Digestive Diseases, Beijing, 100050, China.
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8
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Zhou D, Qi S, Zhang W, Wu L, Xu A, Li X, Zhang B, Li Y, Jia S, Wang H, Jia J, Ou X, Huang J, You H. Insertion of LINE-1 Retrotransposon Inducing Exon Inversion Causes a Rotor Syndrome Phenotype. Front Genet 2020; 10:1399. [PMID: 32082363 PMCID: PMC7005217 DOI: 10.3389/fgene.2019.01399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Rotor syndrome, a rare autosomal-recessive genetic disorder characterized by conjugated hyperbilirubinemia, is caused by biallelic pathogenic variants in both SLCO1B1 and SLCO1B3 genes. Long interspersed nuclear elements (LINEs) make up about 17% of the human genome and insertion of LINE-1 in genes can result in genetic diseases. In the current study, we examined SLCO1B1 and SLCO1B3 genes in two Chinese patients diagnosed with Rotor syndrome based on laboratory tests. In one patient, a novel exon 4 inversion variant was identified. This variant may have been induced by LINE-1 retrotransposon insertion into SLCO1B3 intron 3, and was identified using genome walking. Splicing assay results indicated that the exon inversion, resulting in SLCO1B3 exon 4 (122 bp) exclusion in the mature mRNA, might generate a premature termination codon. Here, we describe an exon inversion contributing to the molecular etiology of Rotor syndrome. Our results may inform future diagnoses and guide drug prescriptions and genetic counseling.
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Affiliation(s)
- Donghu Zhou
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Saiping Qi
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Wei Zhang
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Lina Wu
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Anjian Xu
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Xiaojin Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Bei Zhang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Yanmeng Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Siyu Jia
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Hejing Wang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China
| | - Jidong Jia
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Xiaojuan Ou
- Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Jian Huang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
| | - Hong You
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Beijing, China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Beijing Friendship Hospital, Beijing, China
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9
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Mehmood A, Khan MT, Kaushik AC, Khan AS, Irfan M, Wei DQ. Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance. Front Bioeng Biotechnol 2019; 7:404. [PMID: 31921809 PMCID: PMC6914729 DOI: 10.3389/fbioe.2019.00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/26/2019] [Indexed: 11/15/2022] Open
Abstract
Pyrazinamide (PZA) is one of the main FDA approved drugs to be used as the first line of defense against Mycobacterium Tuberculosis (MTB). It is activated into pyrazinoic acid (POA) via MTB's pncA gene-encoded pyrazinamidase (PZase). Mutations are most commonly responsible for PZA-resistance in nearly 70% of the resistant samples. In the present work, MTB positive samples were chosen for PZA drug susceptibility testing (DST) against critical concentration (100 ug/ml) of PZA. The resistant samples were subjected to pncA sequencing. As a result, 36 various mutations have been observed in the PZA resistant samples, uploaded to the NCBI (GeneBank accession no. MH461111). Here we report the mechanism of PZA resistance behind the three mutants (MTs), Asp12Ala, Pro54Leu, and His57Pro in comparison with the wild type (WT) through molecular dynamics simulation to unveil how these mutations affect the overall conformational stability. The post-simulation analyses revealed notable deviations as compared to the WT structure. Molecular docking studies of PZA with MTs and WT, pocket volume inspection and overall shape complementarity analysis confirmed the deleterious nature of these mutations and gave an insight into the mechanism behind PZA-resistance. These analyses provide vital information regarding MTB drug resistance and could be extremely useful in therapy management and overcoming its global burden.
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Affiliation(s)
- Aamir Mehmood
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | | | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Muhammad Irfan
- Department of Microbiology and Cell Science, Genetics Institute and Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Dong-Qing Wei
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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10
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Khan MT, Malik SI. Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance. J Biomol Struct Dyn 2019; 38:3003-3017. [PMID: 31357912 DOI: 10.1080/07391102.2019.1650113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis (anti-TB) drugs. The anti-TB agent is activated into an active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoding pyrazinamidase (PZase). The major cause of PZA-resistance has been associated with mutations in the pncA gene. We have detected several novel mutations including V131F, Q141P, R154T, A170P, and V180F (GeneBank Accession No. MH461111) in the pncA gene of PZA-resistant isolates during PZA drug susceptibility testing followed by pncA gene sequencing. Here, we investigated molecular mechanism of PZA-resistance by comparing the results of experimental and molecular dynamics. The mutants (MTs) and wild type (WT) PZase structures in apo and complex with PZA were subjected to molecular dynamic simulations (MD) at the 40 ns. Multiple factors, including root mean square deviations (RMSD), binding pocket, total energy, dynamic cross correlation, and root mean square fluctuations (RMSF) of MTs and WT were compared. The MTs attained a high deviation and fluctuation compared to WT. Binding pocket volumes of the MTs, were found, lower than the WT, and the docking scores were high than WT while shape complementarity scores were lower than that of the WT. Residual motion in MTs are seemed to be dominant in anti-correlated motion. Mutations at locations, V131F, Q141P, R154T, A170P, and V180F, might be involved in the structural changes, possibly affecting the catalytic property of PZase to convert PZA into POA. Our study provides useful information that will enhance the understanding for better management of TB. AbbreviationsDSTdrug susceptibility testingΔelecelectrostatic energyLJLowenstein-Jensen mediumMGITmycobacterium growth indicator tubesMTsmutantsMDmolecular dynamic simulationsMTBMycobacterium tuberculosisNALC-NaOHN-acetyl-l-cysteine-sodium hydroxideNIHNational Institutes of HealthNPTamount of substance (N), pressure (P) temperature (T)NVTmoles (N), volume (V) temperature (T)PZasepyrazinamidaseΔpspolar solvation energyPTRLProvincial Tuberculosis Reference LaboratoryRMSDroot mean square deviationsRMSFroot mean square fluctuationsΔSASAsolvent accessible surface area energyTBtuberculosisGTotaltotal binding free energyΔvdWVan der Waals energyWTwild typeCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
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11
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Khan MT, Khan A, Rehman AU, Wang Y, Akhtar K, Malik SI, Wei DQ. Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance. Sci Rep 2019; 9:7482. [PMID: 31097767 PMCID: PMC6522564 DOI: 10.1038/s41598-019-44013-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/29/2019] [Indexed: 02/04/2023] Open
Abstract
Resistance to key first-line drugs is a major hurdle to achieve the global end tuberculosis (TB) targets. A prodrug, pyrazinamide (PZA) is the only drug, effective in latent TB, recommended in drug resistance and susceptible Mycobacterium tuberculosis (MTB) isolates. The prodrug conversion into active form, pyrazinoic acid (POA), required the activity of pncA gene encoded pyrazinamidase (PZase). Although pncA mutations have been commonly associated with PZA resistance but a small number of resistance cases have been associated with mutationss in RpsA protein. Here in this study a total of 69 PZA resistance isolates have been sequenced for pncA mutations. However, samples that were found PZA resistant but pncA wild type (pncAWT), have been sequenced for rpsA and panD genes mutation. We repeated a drug susceptibility testing according to the WHO guidelines on 18 pncAWT MTB isolates. The rpsA and panD genes were sequenced. Out of total 69 PZA resistant isolates, 51 harbored 36 mutations in pncA gene (GeneBank Accession No. MH46111) while, fifteen different mutations including seven novel, were detected in the fourth S1 domain of RpsA known as C-terminal (MtRpsACTD) end. We did not detect any mutations in panD gene. Among the rpsA mutations, we investigated the molecular mechanism of resistance behind mutations, D342N, D343N, A344P, and I351F, present in the MtRpsACTD through molecular dynamic simulations (MD). WT showed a good drug binding affinity as compared to mutants (MTs), D342N, D343N, A344P, and I351F. Binding pocket volume, stability, and fluctuations have been altered whereas the total energy, protein folding, and geometric shape analysis further explored a significant variation between WT and MTs. In conclusion, mutations in MtRpsACTD might be involved to alter the RpsA activity, resulting in drug resistance. Such molecular mechanism behind resistance may provide a better insight into the resistance mechanism to achieve the global TB control targets.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Abbas Khan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Ashfaq Ur Rehman
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Wang
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Khalid Akhtar
- National University of Science and Technology, Islamabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.
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12
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Rehman AU, Khan MT, Liu H, Wadood A, Malik SI, Chen HF. Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 of Mycobacterium tuberculosis. J Chem Inf Model 2019; 59:1584-1597. [DOI: 10.1021/acs.jcim.8b00956] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Biotechnology, Abdul Wali Khan University Marden, Mardan 23200, Pakistan
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Abdul Wadood
- Department of Biotechnology, Abdul Wali Khan University Marden, Mardan 23200, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai, 200235, China
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13
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Li X, Zhang W, Zhou D, Lv T, Xu A, Wang H, Zhao X, Zhang B, Li Y, Jia S, Wang Y, Wang X, Wu Z, Duan W, Wang Q, Nan Y, Shang J, Jiang W, Chen Y, Zheng S, Liu M, Sun L, You H, Jia J, Ou X, Huang J. Complex ATP7B mutation patterns in Wilson disease and evaluation of a yeast model for functional analysis of variants. Hum Mutat 2019; 40:552-565. [PMID: 30702195 DOI: 10.1002/humu.23714] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/16/2022]
Abstract
Wilson disease (WD) is a rare autosomal recessive genetic disorder that is associated with various mutations in the ATP7B gene. Although ATP7B variants are frequently identified, the exact mutation patterns remain unknown because of the absence of pedigree studies, and the functional consequences of individual ATP7B variants remain to be clarified. In this study, we recruited 65 clinically diagnosed WD patients from 60 unrelated families. Pedigree analysis showed that besides several ATP7B homozygous variants (8/65, 12.3%), compound heterozygous variants (43/65, 66.2%) were present in the majority of WD patients. There were 20% of the patients had one (12/65, 18.5%) or multiple (1/65, 1.5%) variants in only a single allele, characterized by a high ratio of splicing or frameshift variants. Nine ATP7B variants were cloned into the pAG426GPD yeast expression vector to evaluate their functional consequences, and the results suggested different degrees of functional disruption from mild or uncertain to severe, consistent with the corresponding phenotypes. Our study revealed the complex ATP7B mutation patterns in WD patients and the applicability of a yeast model system to the evaluation of the functional consequences of ATP7B variants, which is essential for WD cases that are difficult to interpret.
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Affiliation(s)
- Xiaojin Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Wei Zhang
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Donghu Zhou
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Tingxia Lv
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Anjian Xu
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Hejing Wang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Xinyan Zhao
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Bei Zhang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Yanmeng Li
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Siyu Jia
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Yu Wang
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Xiaoming Wang
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Zhen Wu
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Weijia Duan
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Qianyi Wang
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Yuemin Nan
- Department of Traditional and Western Medical Hepatology, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jia Shang
- Department of Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Wei Jiang
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yongpeng Chen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Sujun Zheng
- Artificial Liver Center, Beijing You-An Hospital, Capital Medical University, Beijing, China
| | - Mei Liu
- Artificial Liver Center, Beijing You-An Hospital, Capital Medical University, Beijing, China
| | - Liying Sun
- Liver Transplant Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong You
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Jidong Jia
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Xiaojuan Ou
- Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
| | - Jian Huang
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Translational Medicine on Liver Cirrhosis, Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Clinical Research Center for Rare Liver Diseases, Capital Medical University, Beijing, China.,Liver Research Center, National Clinical Research Center for Digestive Diseases, Beijing, China
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14
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Khan MT, Malik SI, Ali S, Masood N, Nadeem T, Khan AS, Afzal MT. Pyrazinamide resistance and mutations in pncA among isolates of Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan. BMC Infect Dis 2019; 19:116. [PMID: 30728001 PMCID: PMC6364397 DOI: 10.1186/s12879-019-3764-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 01/30/2019] [Indexed: 08/30/2023] Open
Abstract
Background Pyrazinamide (PZA) is an important component of first-line drugs because of its distinctive capability to kill subpopulations of persistent Mycobacterium tuberculosis (MTB). The prodrug (PZA) is converted to its active form, pyrazinoic acid (POA) by MTB pncA-encoded pyrazinamidase (PZase). Mutation in pncA is the most common and primary cause of PZA resistance. The aim of the present study was to explore the molecular characterization of PZA resistance in a Pashtun-dominated region of Khyber Pakhtunkhwa, Pakistan. Methods We performed drug susceptibility testing (DST) on 753 culture-positive isolates collected from the Provincial Tuberculosis Control Program Khyber Pakhtunkhwa using the BACTEC MGIT 960 PZA method. In addition, the pncA gene was sequenced in PZA-resistant isolates, and PZA susceptibility testing results were used to determine the sensitivity and specificity of pncA gene mutations. Results A total of 69 isolates were PZA resistant (14.8%). Mutations were investigated in 69 resistant, 26 susceptible and one H37Rv isolates by sequencing. Thirty-six different mutations were identified in PZA-resistant isolates, with fifteen mutations, including 194_203delCCTCGTCGTG and 317_318delTC, that have not been reported in TBDRM and GMTV Databases and previous studies. Mutations Lys96Thr and Ser179Gly were found in the maximum number of isolates (n = 4 each). We did not detect mutations in sensitive isolates, except for the synonymous mutation 195C > T (Ser65Ser). The sensitivity and specificity of the pncA sequencing method were 79.31% (95% CI, 69.29 to 87.25%) and 86.67% (95% CI, 69.28 to 96.24%). Conclusion Mutations in the pncA gene in circulating isolates of geographically distinct regions, especially in high-burden countries, should be investigated for better control and management of drug-resistant TB. Molecular methods for the investigation of PZA resistance are better than DST.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad Expressway, Kahuta Road, Zone-V, Islamabad, Pakistan.
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad Expressway, Kahuta Road, Zone-V, Islamabad, Pakistan
| | - Sajid Ali
- Department of Microbiology, Quaid-E-Azam University Islamabad and Provincial Tuberculosis Reference, Laboratory Hayatabad Medical Complex, Peshawar, Pakistan
| | - Nayyer Masood
- Department of Computer Science, Capital University of Science and Technology, Islamabad, Pakistan
| | - Tariq Nadeem
- National Center of Excellence in Molecular Biology, University of The Punjab, Lahore, Pakistan
| | - Anwar Sheed Khan
- Institute of Basic Medical Sciences, Khyber Medical University and Provincial Tuberculosis Control Laboratory Hayatabad Medical Complex Peshawar, Peshawar, Pakistan
| | - Muhammad Tanvir Afzal
- Department of Computer Science, Capital University of Science and Technology, Islamabad, Pakistan
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15
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Elango T, Sun J, Zhu C, Zhou F, Zhang Y, Sun L, Yang S, Zhang X. Mutational analysis of epidermal and hyperproliferative type I keratins in mild and moderate psoriasis vulgaris patients: a possible role in the pathogenesis of psoriasis along with disease severity. Hum Genomics 2018; 12:27. [PMID: 29784039 PMCID: PMC5963134 DOI: 10.1186/s40246-018-0158-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/09/2018] [Indexed: 02/08/2023] Open
Abstract
Background Mutations in keratin proteins have been vastly associated with a wide array of genodermatoses; however, mutations of keratins in psoriasis have not been fully investigated. The main aim of the current research was to identify the mutation in K14, K10, K16, and K17 genes in two stages of psoriasis patients. Methods Ninety-six psoriatic skin biopsies were collected. mRNA transcript of K14, K10, K16, and K17 was prepared, amplified, and sequenced. Sanger sequences of all keratins were further validated for mutational analysis using Mutation Surveyor and Alamut Visual. Then, in silico analysis of protein stability and protein and gene expression of all keratins was performed and validated. Results Out of 44 mutations, about 75% of keratins are highly pathogenic and deleterious. Remaining 25% mutations are less pathogenic and tolerated in nature. In these 33 deleterious mutations were immensely found to decrease keratin protein stability. We also found a correlation between keratin and Psoriasis Area and Severity Index score which added that alteration in keratin gene in skin causes severity of psoriasis. Conclusions We strongly concluded that acanthosis and abnormal terminal differentiation was mainly due to the mutation in epidermal keratins. In turn, disease severity and relapsing of psoriasis are mainly due to the mutation of hyperproliferative keratins. These novel keratin mutations in psoriatic epidermis might be one of the causative factors for psoriasis. Electronic supplementary material The online version of this article (10.1186/s40246-018-0158-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamilselvi Elango
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China. .,Anhui Medical University, 81 Meishan Road, Hefei, Anhui Province, China.
| | - Jingying Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Caihong Zhu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Fusheng Zhou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Yaohua Zhang
- Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Liangdan Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, China
| | - Sen Yang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, China
| | - Xuejun Zhang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, China. .,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China. .,Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, China. .,Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai, China. .,Anhui Medical University, 81 Meishan Road, Hefei, Anhui Province, China.
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16
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Impact of annotation error in α-globin genes on molecular diagnosis. PLoS One 2017; 12:e0185270. [PMID: 29049312 PMCID: PMC5648127 DOI: 10.1371/journal.pone.0185270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/08/2017] [Indexed: 11/21/2022] Open
Abstract
Background Recent studies on the variants in duplicated human alpha globin genes (HBA2 and HBA1) actively target the α-globin gene as molecular modulators for the treatment of β-thalassemia major. Identification of the exact position of variant in HBA1, HBA2 or its patchworks is mandatory to support the therapeutic aims in β-thalassemia major, by identifying specific modulators for the reactivation of fetal hemoglobin production. Hence, accurate identification of the variants in α-globin genes is crucial for the proper diagnosis, treatment and genetic counseling. Method The objective was to reveal the annotation errors produced in α-globin gene sequence analysis while using different analytic tools. An HBA2 gene sequence with the HBA2:c.95+2_95+6delTGAGG variant and a recently reported HBA12 gene convert have been taken as examples to prove annotation error in α-globin gene from different analytic tools. Results and discussion Although various bioinformatics tools used to predict variants are usually of high reliability, the current study using the an alpha globin 2 sequence with the HBA2:c.95+2_95+6delTGAGG variant and a recently reported HBA12 gene convert, has showcased ambiguous outputs among the three bioinformatics tools used and against the manual analytical method adopted. Conclusions This report emphasizes the necessity for caution in the usage of DNA sequence analysis tools during molecular diagnosis and the importance of the selection of more appropriate tools for analysis. Furthermore, ethnic specific sequences should be considered as reference sequence for the analysis to bypass sequence dissimilarities among diverse populations.
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17
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Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, Marton T, Krüger M, Fuchs J, Brachmann A, Corradi N. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 2016; 1:16033. [PMID: 27572831 DOI: 10.1038/nmicrobiol.2016.33] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex(1), but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate(2,3). Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.
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Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jessica Noel
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Philippe Charron
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228 Plan-les-Ouates, Switzerland
| | - Timea Marton
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Manuela Krüger
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.,Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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18
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Kimura H, Tsuboi D, Wang C, Kushima I, Koide T, Ikeda M, Iwayama Y, Toyota T, Yamamoto N, Kunimoto S, Nakamura Y, Yoshimi A, Banno M, Xing J, Takasaki Y, Yoshida M, Aleksic B, Uno Y, Okada T, Iidaka T, Inada T, Suzuki M, Ujike H, Kunugi H, Kato T, Yoshikawa T, Iwata N, Kaibuchi K, Ozaki N. Identification of Rare, Single-Nucleotide Mutations in NDE1 and Their Contributions to Schizophrenia Susceptibility. Schizophr Bull 2015; 41:744-53. [PMID: 25332407 PMCID: PMC4393687 DOI: 10.1093/schbul/sbu147] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Nuclear distribution E homolog 1 (NDE1), located within chromosome 16p13.11, plays an essential role in microtubule organization, mitosis, and neuronal migration and has been suggested by several studies of rare copy number variants to be a promising schizophrenia (SCZ) candidate gene. Recently, increasing attention has been paid to rare single-nucleotide variants (SNVs) discovered by deep sequencing of candidate genes, because such SNVs may have large effect sizes and their functional analysis may clarify etiopathology. METHODS AND RESULTS We conducted mutation screening of NDE1 coding exons using 433 SCZ and 145 pervasive developmental disorders samples in order to identify rare single nucleotide variants with a minor allele frequency ≤5%. We then performed genetic association analysis using a large number of unrelated individuals (3554 SCZ, 1041 bipolar disorder [BD], and 4746 controls). Among the discovered novel rare variants, we detected significant associations between SCZ and S214F (P = .039), and between BD and R234C (P = .032). Furthermore, functional assays showed that S214F affected axonal outgrowth and the interaction between NDE1 and YWHAE (14-3-3 epsilon; a neurodevelopmental regulator). CONCLUSIONS This study strengthens the evidence for association between rare variants within NDE1 and SCZ, and may shed light into the molecular mechanisms underlying this severe psychiatric disorder.
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Affiliation(s)
- Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Tsuboi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chenyao Wang
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takayoshi Koide
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoshimi Iwayama
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Noriko Yamamoto
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Shohko Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukako Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Yoshimi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Banno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jingrui Xing
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuto Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mami Yoshida
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan;
| | - Yota Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Iidaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshiya Inada
- Department of Psychiatry, Seiwa Hospital, Institute of Neuropsychiatry, Shinjuku, Tokyo, Japan
| | - Michio Suzuki
- Department of Neuropsychiatry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroshi Ujike
- Department of Psychiatry, Ujike Nishiguchi Clinic (HU), Okayama, Japan
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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19
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Pang R, Li Y, Dong Y, Liang Z, Zhang Y, Zhang W. Identification of promoter polymorphisms in the cytochrome P450 CYP6AY1 linked with insecticide resistance in the brown planthopper, Nilaparvata lugens. INSECT MOLECULAR BIOLOGY 2014; 23:768-778. [PMID: 25124988 DOI: 10.1111/imb.12121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Imidacloprid resistance in the brown planthopper, Nilaparvata lugens, is primarily the result of the over-expression of cytochrome P450 monooxygenases. Here, a field-collected strain of N. lugens was shown to be highly resistant to both imidacloprid and buprofezin. Insecticide exposure and quantitative real-time PCR revealed that its resistance was mainly associated with a cytochrome P450 gene, CYP6AY1. CYP6AY1 is known to metabolize imidacloprid but its effect on buprofezin is unclear. In the 5'-untranslated region of CYP6AY1, a novel alternative splicing was detected. After a 1990-bp promoter region was cloned, its basal luciferase activity was assessed. Furthermore, genotyping studies identified 12 variations in the promoter region that discriminated between the field-collected and control strain. Finally, survival bioassays revealed a single nucleotide polymorphism and an insertion-deletion polymorphism linked to buprofezin and imidacloprid resistance. Mutagenesis of these sites enhanced the promoter activity of CYP6AY1. These results suggest that promoter polymorphisms may affect P450-mediated multiple insecticide resistance of pests.
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Affiliation(s)
- R Pang
- Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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20
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Padula MC, Martelli G, Larocca M, Rossano R, Olivieri A. A novel homozygous stop-codon mutation in human HFE responsible for nonsense-mediated mRNA decay. Blood Cells Mol Dis 2014; 53:138-43. [PMID: 24920245 DOI: 10.1016/j.bcmd.2014.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 12/12/2022]
Abstract
HFE-hemochromatosis (HH) is an autosomal disease characterized by excessive iron absorption. Homozygotes for H63D variant, and still less H63D heterozygotes, generally do not express HH phenotype. The data collected in our previous study in the province of Matera (Basilicata, Italy) underlined that some H63D carriers showed altered iron metabolism, without additional factors. In this study, we selected a cohort of 10/22 H63D carriers with severe biochemical iron overload (BIO). Additional analysis was performed for studying HFE exons, exon-intron boundaries, and untranslated regions (UTRs) by performing DNA extraction, PCR amplification and sequencing. The results showed a novel substitution (NM_000410.3:c.847C>T) in a patient exon 4 (GenBankJQ478433); it introduces a premature stop-codon (PTC). RNA extraction and reverse-transcription were also performed. Quantitative real-time PCR was carried out for verifying if our aberrant mRNA is targeted for nonsense-mediated mRNA decay (NMD); we observed that patient HFE mRNA was expressed much less than calibrator, suggesting that the mutated HFE protein cannot play its role in iron metabolism regulation, resulting in proband BIO. Our finding is the first evidence of a variation responsible for a PTC in iron cycle genes. The genotype-phenotype correlation observed in our cases could be related to the additional mutation.
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Affiliation(s)
- Maria Carmela Padula
- Department of Science, University of Basilicata, Viale dell'Ateneo Lucano, 85100 Potenza, Italy.
| | - Giuseppe Martelli
- Department of Science, University of Basilicata, Viale dell'Ateneo Lucano, 85100 Potenza, Italy
| | - Marilena Larocca
- Department of Science, University of Basilicata, Viale dell'Ateneo Lucano, 85100 Potenza, Italy
| | - Rocco Rossano
- Department of Science, University of Basilicata, Viale dell'Ateneo Lucano, 85100 Potenza, Italy
| | - Attilio Olivieri
- Clinic of Hematology, Hospital-University Company "Ospedali Riuniti di Ancona", Via Conca, 60126 Ancona, Italy
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21
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Wells R, Trick M, Soumpourou E, Clissold L, Morgan C, Werner P, Gibbard C, Clarke M, Jennaway R, Bancroft I. The control of seed oil polyunsaturate content in the polyploid crop species Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:349-362. [PMID: 24489479 PMCID: PMC3901927 DOI: 10.1007/s11032-013-9954-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/05/2013] [Indexed: 05/18/2023]
Abstract
Many important plant species have polyploidy in their recent ancestry, complicating inferences about the genetic basis of trait variation. Although the principal locus controlling the proportion of polyunsaturated fatty acids (PUFAs) in seeds of Arabidopsis thaliana is known (fatty acid desaturase 2; FAD2), commercial cultivars of a related crop, oilseed rape (Brassica napus), with very low PUFA content have yet to be developed. We showed that a cultivar of oilseed rape with lower than usual PUFA content has non-functional alleles at three of the four orthologous FAD2 loci. To explore the genetic basis further, we developed an ethyl methanesulphonate mutagenised population, JBnaCAB_E, and used it to identify lines that also carried mutations in the remaining functional copy. This confirmed the hypothesised basis of variation, resulting in an allelic series of mutant lines showing a spectrum of PUFA contents of seed oil. Several lines had PUFA content of ~6 % and oleic acid content of ~84 %, achieving a long-standing industry objective: very high oleic, very low PUFA rapeseed without the use of genetic modification technology. The population contains a high rate of mutations and represents an important resource for research in B. napus.
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Affiliation(s)
- Rachel Wells
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Leah Clissold
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Colin Morgan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Peter Werner
- KWS UK Ltd., 56 Church Street, Thriplow, Hertfordshire, SG8 7RE UK
| | - Carl Gibbard
- KWS UK Ltd., 56 Church Street, Thriplow, Hertfordshire, SG8 7RE UK
| | | | - Richard Jennaway
- Saaten-Union UK Ltd., Rosalie Field Station, Bradley Road, Cowlinge, Newmarket, Suffolk, CB8 9HU UK
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: Department of Biology, University of York, Heslington, York, YO41 5DD UK
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22
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Abstract
TILLING is widely used in plant functional genomics. Mutagenesis and SNP detection is combined to allow for the isolation of mutations in genes of interest. It can also be used as a plant breeding tool, whereby variation in known or candidate genes of interest to breeding programs is generated. Here we describe a simple low-cost TILLING procedure.
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Affiliation(s)
- Peter Sharp
- Plant Breeding Institute, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
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