1
|
Cao H, Zhang X, Li F, Han Z, Ding B. A point mutation in the IAA14 promoter enhances callus formation and regeneration. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1253-1263. [PMID: 39184564 PMCID: PMC11341521 DOI: 10.1007/s12298-024-01493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 08/27/2024]
Abstract
Callus formation induced by auxin accumulation is considered the first step of in vitro plant regeneration. In Arabidopsis, degradation of the Aux/IAA protein, IAA14, in response to auxin signaling, which activates the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 along with a series of downstream transcription factors, also plays a critical role in this process. However, the specific mechanism by which auxin regulates callus formation remains unclear. By screening mutant library in the solitary root 1 (iaa14/slr) Arabidopsis background we obtained the callus formation related 2 (cfr2) mutant. The cfr2 mutant exhibited a stronger capacity for callus formation, as well as lateral root and adventitious root regeneration from leaf explants than wild type (WT) seedlings, but did not recover gravitropism capability. The auxin signal in cfr2 was significantly enhanced, and the expression of some downstream transcription factors was increased. Map-based cloning, whole genome resequencing, and phenotypic complementation experiments showed that the phenotypes observed in the cfr2 mutant were caused by a point mutation in the IAA14 promoter region. This mutation, which is predicted to disrupt the binding of LBD16, LBD19, and LBD30 to the IAA14 promoter, changed the expression pattern of IAA14 in cfr2. Taken together, our results identified a new mutation in the IAA14 promoter region, which affects the expression pattern of IAA14 and in turn its ability to control plant regeneration. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01493-y.
Collapse
Affiliation(s)
- Huifen Cao
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Xiao Zhang
- Engineering Research Center of Coal-based Ecological Carbon Sequestration Technology of the Ministry of Education, Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Feng Li
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Zhiping Han
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, College of Agriculture and Life Science, Shanxi Datong University, Datong, 037009 Shanxi Province China
| | - Baopeng Ding
- Engineering Research Center of Coal-based Ecological Carbon Sequestration Technology of the Ministry of Education, Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry, Shanxi Datong University, Datong, 037009 Shanxi Province China
| |
Collapse
|
2
|
Mahmood AH, Al-Awadi SJ, Hadi NA, Al-Attar MM. The study of single nucleotide polymorphism in a promoter region of ACE-2 receptor gene in the samples of Iraqi population with COVID-19. Mol Biol Rep 2024; 51:839. [PMID: 39042234 DOI: 10.1007/s11033-024-09785-y] [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: 05/26/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024]
Abstract
BACKGROUND Angiotensin-converting enzyme 2 (ACE2) is an essential receptor on the host cell's cell membrane. It's interesting to note that the entry point receptor ACE2 protein and the severe acute respiratory syndrome (SARS) coronavirus are correlated. This study aimed to determine the influence of the ACE gene genotype and explore the effects of genetic variation in the promotor region of the ACE-2 gene receptor in SARS COV-2 patients. METHODS AND RESULTS The 225 participants were categorized into two groups (75 infected and 150 control) according to the results of Real Time -polymerase chain reaction (RT-PCR), IgM, and IgG, also included two types of samples were collected for diagnosis hematological and molecular study. The hematological and biochemical parameters showed significant differences between the two studied groups according to D. dimer, ferritin, lactate dehydrogenase (LDH), C-reactive protein (CRP), white blood cells (WBC), lymphocyte, packed cell volume (PCV) (P˂0.0001), also red blood cell (RBC) (P = 0.0034). While the results of hemoglobin (HB) and platelet displayed non-significant differences between the two groups (p value 0.6811 and 0.9201 respectively). In addition, the sequencing result in the promotor of the ACE-2 gene detected novel eight polymorphisms and recorded them in NCBI under no. (ON959139). CONCLUSIONS The ACE D/D polymorphism associated with increased levels of ACE could represent a genetic risk factor in addition the discovery stems from the prospect that genetic differences could lead to differing responses to COVID-19 therapies.
Collapse
Affiliation(s)
- Ali H Mahmood
- College of Biotechnology, Al-Nahrain University, Baghdad, Iraq
| | - Salwa J Al-Awadi
- Department of Molecular and Medical Genetics Technologies, College of Biotechnology, Al-Nahrain University, Baghdad, Iraq
| | - Noora A Hadi
- Department of Molecular and Medical Genetics Technologies, College of Biotechnology, Al-Nahrain University, Baghdad, Iraq
| | - Marwa M Al-Attar
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq.
| |
Collapse
|
3
|
Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [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: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
Collapse
Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
4
|
Gao X, Pang S, Ding L, Yan H, Cui Y, Yan B. Genetic and functional variants of the TBX20 gene promoter in dilated cardiomyopathy. Mol Genet Genomic Med 2024; 12:e2355. [PMID: 38284443 PMCID: PMC10795084 DOI: 10.1002/mgg3.2355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a major cause of heart failure and sudden cardiac death. As DCM is a genetically heterogeneous disease, genetic variants of cardiac transcription factor genes may play an important role. Transcription factor TBX20, an indispensable factor in normal heart development, is involved in the regulation of cardiac structure and function. Although the TBX20 gene is associated with the occurrence and development of DCM, the influence of genetic variants of the TBX20 gene promoter region on DCM has not been reported. METHODS We conducted a case-control study consisting of 107 DCM patients and 210 healthy controls. Genetic variants within TBX20 gene promoter region were identified using sequencing techniques and were functionally analyzed by dual-luciferase reporting assay. Electrophoretic mobility shift assay (EMSA) was used to investigate DNA-protein interactions. RESULTS In this study cohort (n = 317), we identified eight variants within TBX20 gene promoter. One novel DNA sequence variants (DSV) (g.4275G>T) and four single-nucleotide polymorphisms (SNPs) [g.4169G>A (rs1263874255), g.4949C>T (rs1191745927), g.5114G>A (rs112076877), g.5252C>T (rs1356932911)] were identified in DCM patients, but in none of controls. Among them, the DSV (g.4275G>T) and three SNPs [g.4949C>T (rs1191745927), g.5114G>A (rs112076877) and g.5252C>T (rs1356932911)] significantly altered the transcription activity of TBX20 gene promoter by dual-luciferase reporting assay (p < 0.05). Further, EMSA assay indicated that the DSV (g.4275G>T) and three SNPs [g.4949C>T (rs1191745927), g.5114G>A (rs112076877) and g.5252C>T (rs1356932911)] affected the binding of transcription factors. CONCLUSIONS These data indicate that the DSV (g.4275G>T) and three SNPs [g.4949C>T (rs1191745927), g.5114G>A (rs112076877) and g.5252C>T (rs1356932911)] increase transcription activity of TBX20 gene promoter in both HEK-293 and neonatal rat cardiomyocytes (NRCMs) cell lines by affecting the binding of transcription factors. But the mechanism remains to be verified in vivo.
Collapse
Affiliation(s)
- Xue Gao
- Cheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Shuchao Pang
- The Center for Molecular Genetics of Cardiovascular DiseasesAffiliated Hospital of Jining Medical University, Jining Medical UniversityJiningShandongChina
- Shandong Provincial Sino‐US Cooperation Research Center for Translational MedicineAffiliated Hospital of Jining Medical University, Jining Medical UniversityJiningShandongChina
| | - Liangcai Ding
- Center for Molecular MedicineYanzhou People's Hospital, Jining Medical UniversityJiningShandongChina
| | - Han Yan
- Center for Molecular MedicineYanzhou People's Hospital, Jining Medical UniversityJiningShandongChina
| | - Yinghua Cui
- Division of CardiologyAffiliated Hospital of Jining Medical University, Jining Medical UniversityJiningShandongChina
| | - Bo Yan
- The Center for Molecular Genetics of Cardiovascular DiseasesAffiliated Hospital of Jining Medical University, Jining Medical UniversityJiningShandongChina
- Shandong Provincial Sino‐US Cooperation Research Center for Translational MedicineAffiliated Hospital of Jining Medical University, Jining Medical UniversityJiningShandongChina
- Center for Molecular MedicineYanzhou People's Hospital, Jining Medical UniversityJiningShandongChina
- Institute of Precision MedicineJining Medical UniversityJiningShandongChina
| |
Collapse
|
5
|
Yin XY, Chen HX, Chen Z, Yang Q, Han J, He GW. Genetic Variants of ISL1 Gene Promoter Identified from Congenital Tetralogy of Fallot Patients Alter Cellular Function Forming Disease Basis. Biomolecules 2023; 13:biom13020358. [PMID: 36830727 PMCID: PMC9953631 DOI: 10.3390/biom13020358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease in newborns. ISL1 is a master transcription factor in second heart field development, whereas the roles of ISL1 gene promoter variants in TOF patients have not been genetically investigated. Total DNA extraction from 601 human subjects, including 308 TOF patients and 293 healthy controls, and Sanger sequencing were performed. Four variants (including one novel heterozygous variant) within the ISL1 gene promoter were only found in TOF patients. Functional analysis of DNA sequence variants was performed by using the dual-luciferase reporter assay and demonstrated that three of the four variants significantly decreased the transcriptional activity of ISL1 gene promoter in HL-1 cells (p < 0.05). Further, the online JASPAR database and electrophoretic mobility shift assay showed that the three variants affected the binding of transcription factors and altered ISL1 expression levels. In conclusion, the current study for the first time demonstrated that the variants identified from the ISL1 gene promoter region are likely involved in the development of TOF by affecting the transcriptional activity and altering the ISL1 expression level. Therefore, these findings may provide new insights into the molecular etiology and potential therapeutic strategy of TOF.
Collapse
Affiliation(s)
- Xiu-Yun Yin
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Zhuo Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Jun Han
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
- Correspondence: or ; Tel.: +86-22-6520-9089
| |
Collapse
|
6
|
Nayarisseri A, Bhrdwaj A, Khan A, Sharma K, Shaheen U, Selvaraj C, Khan MA, Abhirami R, Pravin MA, Shri GR, Raje D, Singh SK. Promoter–motif extraction from co-regulated genes and their relevance to co-expression using E. coli as a model. Brief Funct Genomics 2023; 22:204-216. [PMID: 37053503 DOI: 10.1093/bfgp/elac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/29/2022] [Accepted: 10/26/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
Gene expression varies due to the intrinsic stochasticity of transcription or as a reaction to external perturbations that generate cellular mutations. Co-regulation, co-expression and functional similarity of substances have been employed for indoctrinating the process of the transcriptional paradigm. The difficult process of analysing complicated proteomes and biological switches has been made easier by technical improvements, and microarray technology has flourished as a viable platform. Therefore, this research enables Microarray to cluster genes that are co-expressed and co-regulated into specific segments. Copious search algorithms have been employed to ascertain diacritic motifs or a combination of motifs that are performing regular expression, and their relevant information corresponding to the gene patterns is also documented. The associated genes co-expression and relevant cis-elements are further explored by engaging Escherichia coli as a model organism. Various clustering algorithms have also been used to generate classes of genes with similar expression profiles. A promoter database ‘EcoPromDB’ has been developed by referring RegulonDB database; this promoter database is freely available at www.ecopromdb.eminentbio.com and is divided into two sub-groups, depending upon the results of co-expression and co-regulation analyses.
Collapse
Affiliation(s)
- Anuraj Nayarisseri
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- LeGene Biosciences Pvt Ltd Bioinformatics Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Anushka Bhrdwaj
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Arshiya Khan
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Khushboo Sharma
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Uzma Shaheen
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
| | - Chandrabose Selvaraj
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Mohammad Aqueel Khan
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Rajaram Abhirami
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Muthuraja Arun Pravin
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Gurunathan Rubha Shri
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
| | - Dhanjay Raje
- Eminent Biosciences In silico Research Laboratory, , 91, Sector-A, Mahalakshmi Nagar, Indore, 452010, Madhya Pradesh , India
| | - Sanjeev Kumar Singh
- Alagappa University Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, , Karaikudi, 630003, Tamil Nadu , India
- Department of Data Sciences, Centre of Biomedical Research , SGPGIMS Campus, Raebareli Rd, Lucknow 226014, India
| |
Collapse
|
7
|
Hertzog A, Selvanathan A, Farnsworth E, Tchan M, Adams L, Lewis K, Tolun AA, Bennetts B, Ho G, Bhattacharya K. Intronic variants in inborn errors of metabolism: Beyond the exome. Front Genet 2022; 13:1031495. [PMID: 36561316 PMCID: PMC9763607 DOI: 10.3389/fgene.2022.1031495] [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: 08/30/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Non-coding regions are areas of the genome that do not directly encode protein and were initially thought to be of little biological relevance. However, subsequent identification of pathogenic variants in these regions indicates there are exceptions to this assertion. With the increasing availability of next generation sequencing, variants in non-coding regions are often considered when no causative exonic changes have been identified. There is still a lack of understanding of normal human variation in non-coding areas. As a result, potentially pathogenic non-coding variants are initially classified as variants of uncertain significance or are even overlooked during genomic analysis. In most cases where the phenotype is non-specific, clinical suspicion is not sufficient to warrant further exploration of these changes, partly due to the magnitude of non-coding variants identified. In contrast, inborn errors of metabolism (IEMs) are one group of genetic disorders where there is often high phenotypic specificity. The clinical and biochemical features seen often result in a narrow list of diagnostic possibilities. In this context, there have been numerous cases in which suspicion of a particular IEM led to the discovery of a variant in a non-coding region. We present four patients with IEMs where the molecular aetiology was identified within non-coding regions. Confirmation of the molecular diagnosis is often aided by the clinical and biochemical specificity associated with IEMs. Whilst the clinical severity associated with a non-coding variant can be difficult to predict, obtaining a molecular diagnosis is crucial as it ends diagnostic odysseys and assists in management.
Collapse
Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,*Correspondence: Ashley Hertzog,
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Elizabeth Farnsworth
- Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Michel Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney, NSW, Australia
| | - Louisa Adams
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Katherine Lewis
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Bruce Bennetts
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Gladys Ho
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Kaustuv Bhattacharya
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| |
Collapse
|
8
|
Yin XY, Chen HX, Chen Z, Yang Q, Han J, He GW. Identification and functional analysis of genetic variants of ISL1 gene promoter in human atrial septal defects. J Gene Med 2022; 24:e3450. [PMID: 36170181 DOI: 10.1002/jgm.3450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/16/2022] [Accepted: 09/25/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Atrial septal defect (ASD) is a common type of congenital heart disease. A gene promoter plays pivotal role in the disease development. This study was designed to investigate the pathological role of variants of the ISL1 gene promoter region in ASD patients. METHODS Total DNA extracted from 625 subjects, including 332 ASD patients and 293 healthy controls, was sequenced to identify variants in the promoter region of ISL1 gene. Further functional analyses of the variants were performed with dual luciferase reporter assay and electrophoretic mobility shift assay (EMSA). All possible binding sites of transcription factor affected by the identified variants were predicted using the JASPAR database. RESULTS Four variants in the ISL1 gene promoter were found only in patients with ASD by sequencing. Three of the four variants [g.4923 G > C (rs541081886), g.5079 A > G (rs1371835943) and g.5309 G > A (rs116222082)] significantly decreased the transcriptional activities compared with the wild-type ISL1 gene promoter (p < 0.05). The EMSA revealed that these variants [g.4923 G > C (rs541081886), g.5079 A > G (rs1371835943) and g.5309 G > A (rs116222082)] in the ISL1 gene promoter affected the number and affinity of binding sites of transcription factors. Further analysis with the online JASPAR database demonstrated that a cluster of putative binding sites for transcription factors may be altered by these variants. CONCLUSIONS These sequence variants identified from the promoter region of ISL1 gene in ASD patients are probably involved in the development of ASD by affecting the transcriptional activity and altering ISL1 levels. Therefore, these findings may provide new insights into the molecular etiology and potential therapeutic strategy of ASD.
Collapse
Affiliation(s)
- Xiu-Yun Yin
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui, China & The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Zhuo Chen
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui, China & The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Jun Han
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| |
Collapse
|
9
|
Hassani N, Salmaninejad A, Aslani S, Kamali-sarvestani E, Vessal M. The association between PD-1 gene polymorphisms and susceptibility to multiple sclerosis. Immunol Med 2022; 46:69-76. [PMID: 36308011 DOI: 10.1080/25785826.2022.2137967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Programmed cell death 1 (PD-1) is an immune checkpoint and has been reported to be associated with several autoimmune diseases. We aimed to investigate the association between human PD-1 gene (PDCD1) polymorphisms and multiple sclerosis (MS). This case-control study was conducted on 229 MS patients and 246 healthy controls. Genotyping of rs36084323 (PD-1.1 G/A), rs11568821 (PD-1.3 G/A) and rs2227981 (PD-1.5 C/T) polymorphisms was performed by PCR-RFLP technique. The frequency difference of PD-1.1 genotypes and alleles (-536 G/A) between patients and healthy controls was not significant. Regarding PD-1.3, the AA + AG genotype was found to be relatively higher in the control group. Concerning PD-1.5 (+7785 C/T), the frequency of T allele carriers (TT + CT) was relatively higher in MS patients, which was marginally insignificant (p = .07). PD-1 gene polymorphisms may be associated with MS; however, accurate conclusions require further studies with a larger number of samples.
Collapse
Affiliation(s)
- Nasrin Hassani
- Department of Molecular Biology, Faculty of Medicine, Islamic Azad University, Shiraz, Iran
| | - Arash Salmaninejad
- Regenerative Medicine, Organ Procurement and Transplantation Multi Disciplinary Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Aslani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Eskandar Kamali-sarvestani
- Department of Immunology and Autoimmune Diseases Research Center, Shiraz Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahmood Vessal
- Department of Molecular Biology, Faculty of Medicine, Islamic Azad University, Shiraz, Iran
| |
Collapse
|
10
|
Chen Z, Chen HX, Hou HT, Yin XY, Yang Q, Han J, He GW. Genetic Variants of CITED2 Gene Promoter in Human Atrial Septal Defects: Case-Control Study and Cellular Functional Verification. J Cardiovasc Dev Dis 2022; 9:jcdd9100321. [PMID: 36286273 PMCID: PMC9604052 DOI: 10.3390/jcdd9100321] [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: 09/01/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Atrial septal defect (ASD) is one of the most common forms of congenital heart disease (CHD). Genetic variants in the coding region of the CITED2 gene are known to be significantly correlated with CHD, but the role of variants in the promoter region of CITED2 is unknown. We investigated variants in the promoter of the CITED2 gene in 625 subjects (332 ASD and 293 healthy controls) through Sanger sequencing. Four variants in the CITED2 gene promoter were found only in eight ASD patients with zero occurrence in the control subjects (one case of g.4078A>C(rs1165649373), one case of g.4240C>A(rs1235857801), four cases of g.4935C>T(rs111470468), two cases of g.5027C>T(rs112831934)). Cellular functional analysis showed that these four variants significantly changed the transcriptional activity of the CITED2 gene promoter in HEK-293 and HL-1 cells. Electrophoretic mobility change assay results and JASPAR database analysis demonstrated that these variants created or destroyed a series of possible transcription factor binding sites, resulting in changes in the expression of CITED2 protein. We conclude that the variants of CITED2 promoter in ASD patients affect the transcriptional activity and are likely involved in the occurrence and development of ASD. These findings provide new perspectives on the pathogenesis and potential therapeutic insights of ASD.
Collapse
Affiliation(s)
- Zhuo Chen
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui 241002, China and The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases and Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Hai-Tao Hou
- The Institute of Cardiovascular Diseases and Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Xiu-Yun Yin
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui 241002, China and The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases and Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Jun Han
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui 241002, China
- Correspondence: (J.H.); (G.-W.H.)
| | - Guo-Wei He
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui 241002, China and The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- The Institute of Cardiovascular Diseases and Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University and Chinese Academy of Medical Sciences, Tianjin 300457, China
- Correspondence: (J.H.); (G.-W.H.)
| |
Collapse
|
11
|
Valenzuela-Palomo A, Sanoguera-Miralles L, Bueno-Martínez E, Esteban-Sánchez A, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Gómez-Barrero S, de la Hoya M, Velasco-Sampedro EA. Splicing Analysis of 16 PALB2 ClinVar Variants by Minigene Assays: Identification of Six Likely Pathogenic Variants. Cancers (Basel) 2022; 14:cancers14184541. [PMID: 36139699 PMCID: PMC9496955 DOI: 10.3390/cancers14184541] [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: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
PALB2 loss-of-function variants are associated with significant increased risk of breast cancer as well as other types of tumors. Likewise, splicing disruptions are a common mechanism of disease susceptibility. Indeed, we previously showed, by minigene assays, that 35 out of 42 PALB2 variants impaired splicing. Taking advantage of one of these constructs (mgPALB2_ex1-3), we proceeded to analyze other variants at exons 1 to 3 reported at the ClinVar database. Thirty-one variants were bioinformatically analyzed with MaxEntScan and SpliceAI. Then, 16 variants were selected for subsequent RNA assays. We identified a total of 12 spliceogenic variants, 11 of which did not produce any trace of the expected minigene full-length transcript. Interestingly, variant c.49-1G > A mimicked previous outcomes in patient RNA (transcript ∆(E2p6)), supporting the reproducibility of the minigene approach. A total of eight variant-induced transcripts were characterized, three of which (∆(E1q17), ∆(E3p11), and ∆(E3)) were predicted to introduce a premature termination codon and to undergo nonsense-mediated decay, and five (▼(E1q9), ∆(E2p6), ∆(E2), ▼(E3q48)-a, and ▼(E3q48)-b) maintained the reading frame. According to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, which integrates mgPALB2 data, six PALB2 variants were classified as pathogenic/likely pathogenic, five as VUS, and five as likely benign. Furthermore, five ±1,2 variants were catalogued as VUS because they produced significant proportions of in-frame transcripts of unknown impact on protein function.
Collapse
Affiliation(s)
- Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Susana Gómez-Barrero
- Facultad de Ciencias de la Salud, Universidad Alfonso X “El Sabio”, Avda. de la Universidad 1, Villanueva de la Cañada, 28691 Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Eladio A. Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
- Correspondence:
| |
Collapse
|
12
|
Zeng ZH, Chen HX, Liu XC, Yang Q, He GW. Functional significance of novel variants of the MEF2C gene promoter in congenital ventricular septal defects. Am J Med Genet A 2022; 188:2397-2405. [PMID: 35719119 DOI: 10.1002/ajmg.a.62871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 11/10/2022]
Abstract
Ventricular septal defect (VSD) is the most common congenital heart disease. Although the coding region of MEF2C is highly relevant to cardiac malformations, the role of MEF2C gene promoter variants in VSD patients has not been genetically investigated. We investigated the role of MEF2C gene promoter variants in 400 Han Chinese subjects (200 patients with isolated and sporadic VSD and 200 healthy controls). The promoter region of the MEF2C gene was sequenced that identified 10 variants. Expression vectors encompassing the variants and the firefly luciferase reporter gene plasmid (pGL3-basic) were constructed and subsequently transfected into HEK-293 cells. The luciferase activities were measured by Dual-luciferase reporter assay system. MEF2C gene promoter transcriptional activity was significantly reduced in 4 of the 10 variants in HEK-293 cells (P < 0.05). In addition, the JASPAR database was used to perform bioinformatics analysis, which showed that these variants disrupt the putative binding sites of transcription factors and affected the expression of MEF2C protein. This study for the first time identified the variants in the promoter of the MEF2C gene in Han Chinese population and revealed the role of these variants in the formation of VSD.
Collapse
Affiliation(s)
- Zhi-Hua Zeng
- The Institute of Cardiovascualr Diseases & Department of Cardiovascular surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Graduate School of Peking Union Medical College & Tianjin University, Tianjin, China
| | - Huan-Xin Chen
- The Institute of Cardiovascualr Diseases & Department of Cardiovascular surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Graduate School of Peking Union Medical College & Tianjin University, Tianjin, China
| | - Xiao-Cheng Liu
- The Institute of Cardiovascualr Diseases & Department of Cardiovascular surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Graduate School of Peking Union Medical College & Tianjin University, Tianjin, China
| | - Qin Yang
- The Institute of Cardiovascualr Diseases & Department of Cardiovascular surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Graduate School of Peking Union Medical College & Tianjin University, Tianjin, China
| | - Guo-Wei He
- The Institute of Cardiovascualr Diseases & Department of Cardiovascular surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Graduate School of Peking Union Medical College & Tianjin University, Tianjin, China
| |
Collapse
|
13
|
Valenzuela‐Palomo A, Bueno‐Martínez E, Sanoguera‐Miralles L, Lorca V, Fraile‐Bethencourt E, Esteban‐Sánchez A, Gómez‐Barrero S, Carvalho S, Allen J, García‐Álvarez A, Pérez‐Segura P, Dorling L, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Splicing predictions, minigene analyses, and ACMG-AMP clinical classification of 42 germline PALB2 splice-site variants. J Pathol 2022; 256:321-334. [PMID: 34846068 PMCID: PMC9306493 DOI: 10.1002/path.5839] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022]
Abstract
PALB2 loss-of-function variants confer high risk of developing breast cancer. Here we present a systematic functional analysis of PALB2 splice-site variants detected in approximately 113,000 women in the large-scale sequencing project Breast Cancer After Diagnostic Gene Sequencing (BRIDGES; https://bridges-research.eu/). Eighty-two PALB2 variants at the intron-exon boundaries were analyzed with MaxEntScan. Forty-two variants were selected for the subsequent splicing functional assays. For this purpose, three splicing reporter minigenes comprising exons 1-12 were constructed. The 42 potential spliceogenic variants were introduced into the minigenes by site-directed mutagenesis and assayed in MCF-7/MDA-MB-231 cells. Splicing anomalies were observed in 35 variants, 23 of which showed no traces or minimal amounts of the expected full-length transcripts of each minigene. More than 30 different variant-induced transcripts were characterized, 23 of which were predicted to truncate the PALB2 protein. The pathogenicity of all variants was interpreted according to an in-house adaptation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) variant classification scheme. Up to 23 variants were classified as pathogenic/likely pathogenic. Remarkably, three ±1,2 variants (c.49-2A>T, c.108+2T>C, and c.211+1G>A) were classified as variants of unknown significance, as they produced significant amounts of either in-frame transcripts of unknown impact on the PALB2 protein function or the minigene full-length transcripts. In conclusion, we have significantly contributed to the ongoing effort of identifying spliceogenic variants in the clinically relevant PALB2 cancer susceptibility gene. Moreover, we suggest some approaches to classify the findings in accordance with the ACMG-AMP rationale. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Alberto Valenzuela‐Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Elena Bueno‐Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Lara Sanoguera‐Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Víctor Lorca
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eugenia Fraile‐Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
- Knight Cancer Research BuildingPortlandORUSA
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | | | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Alicia García‐Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Pedro Pérez‐Segura
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Peter Devilee
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maaike PG Vreeswijk
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| |
Collapse
|
14
|
Chen S, Liu S, Mi S, Li W, Zhang S, Ding X, Yu Y. Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development. Front Genet 2021; 12:740036. [PMID: 34691153 PMCID: PMC8527042 DOI: 10.3389/fgene.2021.740036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Identifying epigenetic changes is essential for an in-depth understanding of phenotypic diversity and pigs as the human medical model for anatomizing complex diseases. Abnormal sperm DNA methylation can lead to male infertility, fetal development failure, and affect the phenotypic traits of offspring. However, the whole genome epigenome map in pig sperm is lacking to date. In this study, we profiled methylation levels of cytosine in three commercial pig breeds, Landrace, Duroc, and Large White using whole-genome bisulfite sequencing (WGBS). The results showed that the correlation of methylation levels between Landrace and Large White pigs was higher. We found that 1,040-1,666 breed-specific hypomethylated regions (HMRs) were associated with embryonic developmental and economically complex traits for each breed. By integrating reduced representation bisulfite sequencing (RRBS) public data of pig testis, 1743 conservated HMRs between sperm and testis were defined, which may play a role in spermatogenesis. In addition, we found that the DNA methylation patterns of human and pig sperm showed high similarity by integrating public data from WGBS and chromatin immunoprecipitation sequencing (ChIP-seq) in other mammals, such as human and mouse. We identified 2,733 conserved HMRs between human and pig involved in organ development and brain-related traits, such as NLGN1 (neuroligin 1) containing a conserved-HMR between human and pig. Our results revealed the similarities and diversity of sperm methylation patterns among three commercial pig breeds and between human and pig. These findings are beneficial for elucidating the mechanism of male fertility, and the changes in commercial traits that undergo strong selection.
Collapse
Affiliation(s)
| | | | | | | | | | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
15
|
Growth, Dietary Intake, and Vitamin D Receptor (VDR) Promoter Genotype in Indonesian School-Age Children. Nutrients 2021; 13:nu13092904. [PMID: 34578782 PMCID: PMC8472703 DOI: 10.3390/nu13092904] [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: 07/10/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/03/2022] Open
Abstract
Nutrition has been known as a predominant factor associated with stunting. However, some studies have discovered a genetic contribution in calcium absorption that will affect growth, known as the VDR gene. The aim of this study was to assess the association between VDR gene polymorphism and dietary intake towards height-for-age z-score (HAZ) of elementary school children in Malang District, East Java. This study analyzed the baseline of a randomized trial in East Java, Indonesia. School children aged 8–10 years old (n = 142) were included in this study. Energy, protein, calcium, and vitamin D intakes were obtained using 4-day 24-h dietary recalls. Two SNPs located in the promoter region of VDR gene were selected (rs11568820 and rs4516035) and analyzed using Real-Time PCR. The result showed a significant correlation between energy and protein intake with HAZ of the children (p = 0.030 and p = 0.016, respectively). The association between VDR gene and HAZ was not found (p > 0.05). Adjusted by other factors, protein intake was significantly correlated with HAZ (β = 0.034, 95% CI 0.015–0.052, p < 0.001, adj. R2 = 0.089). The children in our study had a favorable VDR gene genotype, however the effect of VDR gene promoter activity might not be revealed due to very low vitamin D and calcium intake to stimulate intestinal calcium absorption which in turn affects HAZ.
Collapse
|
16
|
Dharmalingam P, Mahalingam R, Yalamanchili HK, Weng T, Karmouty-Quintana H, Guha A, A Thandavarayan R. Emerging roles of alternative cleavage and polyadenylation (APA) in human disease. J Cell Physiol 2021; 237:149-160. [PMID: 34378793 DOI: 10.1002/jcp.30549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022]
Abstract
In the messenger RNA (mRNA) maturation process, the 3'-end of pre-mRNA is cleaved and a poly(A) sequence is added, this is an important determinant of mRNA stability and its cellular functions. More than 60%-70% of human genes have three or more polyadenylation (APA) sites and can be cleaved at different sites, generating mRNA transcripts of varying lengths. This phenomenon is termed as alternative cleavage and polyadenylation (APA) and it plays role in key biological processes like gene regulation, cell proliferation, senescence, and also in various human diseases. Loss of regulatory microRNA binding sites and interactions with RNA-binding proteins leading to APA are largely investigated in human diseases. However, the functions of the core APA machinery and related factors during disease conditions remain largely unknown. In this review, we discuss the roles of polyadenylation machinery in relation to brain disease, cardiac failure, pulmonary fibrosis, cancer, infectious conditions, and other human diseases. Collectively, we believe this review will be a useful avenue for understanding the emerging role of APA in the pathobiology of various human diseases.
Collapse
Affiliation(s)
- Prakash Dharmalingam
- Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai, India
| | - Rajasekaran Mahalingam
- Laboratory of Neuroimmunology, Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics - Neurology, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas, USA
| | - Tingting Weng
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology & Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ashrith Guha
- Department of Cardiology, Houston Methodist DeBakey Heart & Vascular Center, Houston, Texas, USA
| | | |
Collapse
|
17
|
Zheng SQ, Chen HX, Liu XC, Yang Q, He GW. Identification of variants of ISL1 gene promoter and cellular functions in isolated ventricular septal defects. Am J Physiol Cell Physiol 2021; 321:C443-C452. [PMID: 34260301 DOI: 10.1152/ajpcell.00167.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ventricular septal defects (VSDs) are the most common congenital heart defects (CHDs). Studies have documented that ISL1 has a crucial impact on cardiac growth, but the role of variants in the ISL1 gene promoter in patients with VSD has not been explored. In 400 subjects (200 patients with isolated and sporadic VSDs: 200 healthy controls), we investigated the ISL1 gene promoter variant and performed cellular functional experiments by using the dual-luciferase reporter assay to verify the impact on gene expression. In the ISL1 promoter, five variants were found only in patients with VSD by sequencing. Cellular functional experiments demonstrated that three variants decreased the transcriptional activity of the ISL1 promoter (P < 0.05). Further analysis with the online JASPAR database demonstrated that a cluster of putative binding sites for transcription factors may be altered by these variants, possibly resulting in change of ISL1 protein expression and VSD formation. Our study has, for the first time, identified novel variants in the ISL1 gene promoter region in the Han Chinese patients with isolated and sporadic VSD. In addition, the cellular functional experiments, electrophoretic mobility shift assay, and bioinformatic analysis have demonstrated that these variants significantly alter the expression of the ISL1 gene and affect the binding of transcription factors, likely resulting in VSD. Therefore, this study may provide new insights into the role of the gene promoter region for a better understanding of genetic basis of the formation of CHDs and may promote further investigations on mechanism of the formation of CHDs.
Collapse
Affiliation(s)
- Si-Qiang Zheng
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, People's Republic of China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, People's Republic of China
| | - Xiao-Cheng Liu
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, People's Republic of China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, People's Republic of China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, People's Republic of China.,Drug Research and Development Center, Wannan Medical College, Wuhu, People's Republic of China.,Department of Surgery, Oregon Health and Science University, Portland, Oregon
| |
Collapse
|
18
|
Abstract
Abstract
Purpose of Review
Whole exome sequencing (WES) and whole-genome sequencing (WGS) are frontline approaches for the genetic diagnosis of rare diseases. However, WES/WGS fails in up to 75% of cases. Transcriptomics via RNA-sequencing (RNA-Seq) is a novel approach that aims to increase the diagnostic yield in rare diseases.
Recent Findings
Recent publications focus on the success of RNA-Seq for increasing diagnosis rates in WES/WGS-negative patients in up to 36% of cases, across a range of different diseases, sample sizes, and tissue types.
Summary
RNA-Seq is beneficial for aiding prioritisation of causative variants currently not detected or often overlooked by WES/WGS alone. An improvement in diagnostic yields has been demonstrated using multiple source tissues, with muscle and fibroblasts being the most representative, but the more accessible blood still demonstrating diagnostic success, particularly in neuromuscular disorders. The introduction of RNA-Seq to the genetic diagnosis toolbox promises to be a useful complementary tool to WES/WGS for improving genetic diagnosis in patients with rare disease.
Collapse
|
19
|
Machado-Rugolo J, Gutierrez Prieto T, Fabro AT, Parra Cuentas ER, Sá VK, Baldavira CM, Rainho CA, Castelli EC, Farhat C, Takagaki TY, Nagai MA, Capelozzi VL. Relevance of PD-L1 Non-Coding Polymorphisms on the Prognosis of a Genetically Admixed NSCLC Cohort. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:239-252. [PMID: 33623414 PMCID: PMC7894801 DOI: 10.2147/pgpm.s286717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/14/2021] [Indexed: 12/25/2022]
Abstract
Purpose Although non-small cell lung cancer (NSCLC) remains a deadly disease, new predictive biomarkers have emerged to assist in managing the disease, of which one of the most promising is the programmed death‐ligand 1 (PD-L1). Each, PD-L1 variant seem to modulate the function of immune checkpoints differently and affect response to adjuvant treatment and outcome in NSCLC patients. We thus investigated the influence of these PD-L1 genetic variations in genetically admixed NSCLC tissue samples, and correlated these values with clinicopathological characteristics, including prognosis. Materials and Methods We evaluated PD-L1 non-coding genetic variants and protein expression in lung adenocarcinomas (ADC), squamous cell carcinomas (SqCC), and large cell carcinomas (LCC) in silico. Microarray paraffin blocks from 70 samples of ADC (N=33), SqCC (N=24), and LCC (N=13) were used to create PD-L1 multiplex immunofluorescence assays with a Cell Signaling E1L3N clone. Fifteen polymorphisms of the PD-L1 gene were investigated by targeted sequencing and evaluated in silico using dedicated tools. Results Although PD-L1 polymorphisms seemed not to interfere with protein expression, PD-L1 expression varied among different histological subtypes, as did clinical outcomes, with the rs4742098A>G, rs4143815G>C, and rs7041009G>A variants being associated with relapse (P=0.01; P=0.05; P=0.02, respectively). The rs7041009 GG genotype showed a significant correlation with younger and alive patients compared to carriers of the A allele (P=0.02 and P<0.01, respectively). The Cox regression model showed that the rs7041009 GG genotype may influence OS (P<0.01) as a co-dependent factor associated with radiotherapy and recurrence in NSCLC patients. Furthermore, the Kaplan–Meier survival curves showed that rs7041009 and rs4742098 might impact PPS in relapsed patients. In silico approaches identified the variants as benign. Conclusion PD-L1 non-coding variants play an important role in modulating immune checkpoint function and may be explored as immunotherapy biomarkers. We highlight the rs7041009 variant, which impacts OS and PPS in NSCLC patients.
Collapse
Affiliation(s)
- Juliana Machado-Rugolo
- Laboratory of Genomics and Histomorphometry, Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil.,Health Technology Assessment Center, Clinical Hospital (HCFMB), Medical School of São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Tabatha Gutierrez Prieto
- Laboratory of Genomics and Histomorphometry, Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil
| | - Alexandre Todorovic Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto School of Medicine, University of São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | - Edwin Roger Parra Cuentas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vanessa Karen Sá
- Laboratory of Genomics and Molecular Biology, Centro Internacional De Pesquisa (CIPE), AC Camargo Cancer Center, São Paulo, SP, Brazil
| | - Camila Machado Baldavira
- Laboratory of Genomics and Histomorphometry, Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil
| | - Claudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), Medical School of São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Department of Pathology, Medical School of São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Cecilia Farhat
- Laboratory of Genomics and Histomorphometry, Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil
| | - Teresa Yae Takagaki
- Division of Pneumology, Heart Institute (Incor), Clinical Hospital, University of São Paulo Medical School (USP), São Paulo, São Paulo, Brazil
| | - Maria Aparecida Nagai
- Department of Radiology and Oncology, University of São Paulo Medical School (USP), São Paulo, Brazil.,Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of São Paulo (ICESP), São Paulo, Brazil
| | - Vera Luiza Capelozzi
- Laboratory of Genomics and Histomorphometry, Department of Pathology, University of São Paulo Medical School (USP), São Paulo, Brazil
| |
Collapse
|
20
|
Zheng SQ, Chen HX, Liu XC, Yang Q, He GW. Genetic analysis of the CITED2 gene promoter in isolated and sporadic congenital ventricular septal defects. J Cell Mol Med 2021; 25:2254-2261. [PMID: 33439552 PMCID: PMC7882930 DOI: 10.1111/jcmm.16218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 12/22/2022] Open
Abstract
Ventricular septal defect (VSD) is the most common congenital heart defect. Previous studies have reported genetic variations in the encoding region of CITED2 highly associated with cardiac malformation but the role of CITED2 gene promoter variations in VSD patients has not yet been explored. We investigated the variation of CITED2 gene promoter and its impacts on gene promoter activity in the DNA of paediatric VSD patients. A total of seven variations were identified by Sanger sequencing in the CITED2 gene promoter region in 400 subjects, including 200 isolated and sporadic VSD patients and 200 healthy controls. Using dual‐luciferase reporter assay, we found four of the 7 variations identified significantly decreased the transcriptional activity of the CITED2 gene promoter in HEK‐293 cells (P < .05). Further, a bioinformatic analysis with the JASPAR databases was performed and a cluster of putative binding sites for transcription factors was created or disrupted by these variations, leading to low expression of CITED2 protein and development of VSD. Our study for the first time demonstrates genetic variations in the CITED2 gene promoter in the Han Chinese population and the role of these variations in the development of VSD, providing new insights into the aetiology of CHD.
Collapse
Affiliation(s)
- Si-Qiang Zheng
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, & Graduate School of Peking Union Medical College, Tianjin, China
| | - Huan-Xin Chen
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, & Graduate School of Peking Union Medical College, Tianjin, China
| | - Xiao-Cheng Liu
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, & Graduate School of Peking Union Medical College, Tianjin, China
| | - Qin Yang
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, & Graduate School of Peking Union Medical College, Tianjin, China
| | - Guo-Wei He
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, & Graduate School of Peking Union Medical College, Tianjin, China.,The Institute of Cardiovascular Diseases, Tianjin University, Tianjin, China.,Drug Research and Development Center, Wannan Medical College, Wuhu, China.,Department of Surgery, Oregon Health and Science University, Portland, OR, USA
| |
Collapse
|
21
|
Association of XRCC2 rs2040639 with the survival of patients with oral squamous cell carcinoma undergoing concurrent chemoradiotherapy. Gene 2020; 768:145283. [PMID: 33144272 DOI: 10.1016/j.gene.2020.145283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To investigate the association between the variants of DNA double-strand break repair genes and the clinical outcomes of patients with oral squamous cell carcinoma (OSCC) undergoing concurrent chemoradiotherapy. METHODS Five variants of DNA double-strand break repair genes in samples from 319 patients with OSCC were genotyped using the Sequenom iPLEX MassARRAY system. Kaplan-Meier curves and Cox proportional hazards analysis were used to identify the factors associated with patient survival. RESULTS The XRCC2 rs2040639 (G3063A) polymorphism in the codominant model was associated with decreased recurrence risk (hazard ratio [HR] = 0.55, 95% confidence interval [CI] = 0.31-0.98; p = 0.042). A marginally significant interaction was observed between XRCC2 rs2040639 and PRKDC rs7003908 in patients carrying the AA and AA genotypes; these patients showed reduced recurrence risk (HR = 0.36, 95% CI = 0.17-0.79; p = 0.010). CONCLUSION The A-allele of XRCC2 rs2040639 is a favorable prognostic factor for disease-free survival. Patients with these genotypes may benefit from concurrent chemoradiotherapy. Additional confirmation from studies with larger samples or other ethnic populations is warranted.
Collapse
|
22
|
Jung CK, Jung SH, Jeon S, Jeong YM, Kim Y, Lee S, Bae JS, Chung YJ. Risk Stratification Using a Novel Genetic Classifier Including PLEKHS1 Promoter Mutations for Differentiated Thyroid Cancer with Distant Metastasis. Thyroid 2020; 30:1589-1600. [PMID: 32326836 DOI: 10.1089/thy.2019.0459] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background: Although most differentiated thyroid carcinomas (DTCs) have indolent behavior, DTCs with distant metastasis have a poor prognosis. However, there are no validated markers that predict the risk of distant metastasis and the prognosis of DTC. We aimed to develop a genetic classifier for predicting the outcomes of DTC patients with distant metastases. Methods: Targeted deep sequencing of 157 cancer-related genes was performed for 61 DTCs with distant metastases. A candidate mutation was validated with independent thyroid cancer samples using digital polymerase chain reaction. Results: The most frequently mutated gene in the 61 DTCs was BRAF (n = 31, 51%), followed by TERT promoter (n = 28, 46%), NRAS (n = 13, 11%), PLEKHS1 promoter (n = 6, 10%), and STK11 (n = 6, 10%) mutations. PLEKHS1 promoter mutations were more common in the radioactive iodine (RAI)-refractory cases (p = 0.003). Losses of 9q and 11q were associated with RAI-refractory disease (p = 0.002) and cancer-specific mortality (p = 0.028), respectively. In multivariate analysis, bone metastasis (adjusted odds ratio [aOR] = 15.17, 95% confidence interval [CI 3.38-68.06], p < 0.001) and at least one mutation in the TERT promoter, the PLEKHS1 promoter, or TP53 (aOR = 7.64 [CI 1.78-32.76], p = 0.006) remained significant factors associated with RAI-refractoriness. In independently collected papillary thyroid carcinomas without initial distant metastasis (n = 75), a PLEKHS1 promoter mutation was only found in one case that developed distant metastasis during the follow-up period. We developed a genetic classifier consisting of BRAF, RAS, the TERT promoter, the PLEKHS1 promoter, and TP53 for categorizing the prognosis of patients with DTC with distant metastasis. In the poor-prognosis group, 61% of the patients were RAI-refractory and death occurred in 21% during the follow-up. In the intermediate-prognosis group, 29% were RAI-refractory, but no death occurred. In the good-prognosis group, all patients were RAI-responsive and no death occurred. Conclusions: Mutations in the PLEKHS1 promoter are a novel genetic marker of aggressive DTC. Our genetic classifier can be useful for predicting RAI-refractory disease and poor prognosis in DTC patients with distant metastases.
Collapse
Affiliation(s)
- Chan Kwon Jung
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung-Hyun Jung
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sora Jeon
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Young Mun Jeong
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yourha Kim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sohee Lee
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ja-Seong Bae
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- IRCGP, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| |
Collapse
|
23
|
Hitti-Malin RJ, Burmeister LM, Ricketts SL, Lewis TW, Pettitt L, Boursnell M, Schofield EC, Sargan D, Mellersh CS. A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs. BMC Genet 2020; 21:100. [PMID: 32894063 PMCID: PMC7487703 DOI: 10.1186/s12863-020-00911-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 08/30/2020] [Indexed: 12/30/2022] Open
Abstract
Background Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lhasa Apso (LA) dog has not previously been clinically characterised or described in the literature, but owners in the UK are advised to have their dog examined through the British Veterinary Association/ Kennel Club/ International Sheep Dog Society (BVA/KC/ISDS) eye scheme annually, and similar schemes that are in operation in other countries. After the exclusion of 25 previously reported canine retinal mutations in LA PRA-affected dogs, we sought to identify the genetic cause of PRA in this breed. Results Analysis of whole-exome sequencing data of three PRA-affected LA and three LA without signs of PRA did not identify any exonic or splice site variants, suggesting the causal variant was non-exonic. We subsequently undertook a genome-wide association study (GWAS), which identified a 1.3 Mb disease-associated region on canine chromosome 33, followed by whole-genome sequencing analysis that revealed a long interspersed element-1 (LINE-1) insertion upstream of the IMPG2 gene. IMPG2 has previously been implicated in human retinal disease; however, until now no canine PRAs have been associated with this gene. The identification of this PRA-associated variant has enabled the development of a DNA test for this form of PRA in the breed, here termed PRA4 to distinguish it from other forms of PRA described in other breeds. This test has been used to determine the genotypes of over 900 LA dogs. A large cohort of genotyped dogs was used to estimate the allele frequency as between 0.07–0.1 in the UK LA population. Conclusions Through the use of GWAS and subsequent sequencing of a PRA case, we have identified a LINE-1 insertion in the retinal candidate gene IMPG2 that is associated with a form of PRA in the LA dog. Validation of this variant in 447 dogs of 123 breeds determined it was private to LA dogs. We envisage that, over time, the developed DNA test will offer breeders the opportunity to avoid producing dogs affected with this form of PRA.
Collapse
Affiliation(s)
- Rebekkah J Hitti-Malin
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
| | - Louise M Burmeister
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Sally L Ricketts
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Thomas W Lewis
- The Kennel Club, London, W1J 8AB, UK.,School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Louise Pettitt
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Mike Boursnell
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Ellen C Schofield
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - David Sargan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Cathryn S Mellersh
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| |
Collapse
|
24
|
Whole genome sequencing analysis of high confidence variants of B-cell lymphoma in Canis familiaris. PLoS One 2020; 15:e0238183. [PMID: 32857815 PMCID: PMC7454977 DOI: 10.1371/journal.pone.0238183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 08/11/2020] [Indexed: 11/19/2022] Open
Abstract
Lymphoma (lymphosarcoma) is the second most frequent cancer in dogs and is clinically comparable to human non-Hodgkin lymphoma. Factors affecting canine lymphoma progression are unknown and complex, but there is evidence that genetic mutations play an important role. We employed Next Gen DNA sequencing of six dogs with multicentric B-cell lymphoma undergoing CHOP chemotherapy to identify genetic variations potentially impacting response. Paired samples from non-neoplastic tissue (blood mononuclear cells) and lymphoma were collected at the time of diagnosis. Cases with progression free survival above the median of 231 days were grouped as 'good' responders and cases below the median were categorized as 'poor' responders. The average number of variants found was 17,138 per case. The variants were filtered to examine those with predicted moderate or high impacts. Many of the genes with variants had human orthologs with links to cancer, but the majority of variants were not previously reported in canine or human lymphoma. Seven genes had variants found in the cancers of at least two 'poor' responders but in no 'good' responders: ATRNL1, BAIAP2L2, ZNF384, ST6GALNAC5, ENSCAFG00000030179 (human ortholog: riboflavin kinase RFK), ENSCAFG00000029320, and ENSCAFG00000007370 (human ortholog: immunoglobin IGKV4-1). Two genes had variants found in the cancers of at least two 'good' responders but in no 'poor' responders: COX18 and ENSCAFG00000030512. ENSCAFG00000030512 has no reported orthologue in any other species. The role of these mutations in the progression of canine lymphoma requires further functional analyses and larger scale study.
Collapse
|
25
|
Yamamoto M, Kobayashi T, Mashima H, Miki D, Kuroda S, Hamaoka M, Aikata H, Chayama K, Ohdan H. PD1 gene polymorphism is associated with a poor prognosis in hepatocellular carcinoma following liver resection, cohort study. Int J Surg 2020; 80:84-90. [PMID: 32615319 DOI: 10.1016/j.ijsu.2020.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND This study examined whether single nucleotide polymorphism (SNP) in programmed cell death protein (PD)-1 is related to the postoperative prognosis of patients with hepatocellular carcinoma (HCC). The immune checkpoint protein PD-1 is an important inhibitor of T cell responses. SNP in the promoter region of PD-1 -606 G/A has been reported to result in high activation and expression of PD-1 associated with cancer risk. MATERIALS AND METHODS We analyzed 321 patients with HCC who underwent hepatectomy between 2010 and 2015. PD-1 SNP was analyzed by polymerase chain reaction, and the prognosis after surgical treatment of patients with HCC was analyzed. RESULTS The PD-1 SNP statuses were as follows: 90 AA (28.1%), 163 GA (50.8%), 68 GG (21.2%). The baseline parameters did not statistically differ between the three groups. The overall survival (OS) of patients with the GG genotype was significantly lower than that of those with the other genotypes (P = 0.031). The GG genotype was an independent risk factor for OS (P = 0.009; HR 2.201). There was no significant difference between the GG genotype and other genotypes in recurrent-free survival. The extrahepatic recurrence (EHR) rate of those with the GG genotype was significantly higher than that of those with the other genotypes (P = 0.036). The GG genotype was an independent risk factor for EHR (P = 0.008; HR 2.037). CONCLUSIONS The PD-1 SNP GG genotype is associated with poor survival and increased EHR in HCC. Furthermore, the GG genotype is an independent predictive factor for OS and EHR.
Collapse
Affiliation(s)
- Masateru Yamamoto
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Tsuyoshi Kobayashi
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan.
| | - Hiroaki Mashima
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Daiki Miki
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Shintaro Kuroda
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Michinori Hamaoka
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Hideki Ohdan
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan; Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
26
|
Hashemi M, Karami S, Sarabandi S, Moazeni-Roodi A, Małecki A, Ghavami S, Wiechec E. Association between PD-1 and PD-L1 Polymorphisms and the Risk of Cancer: A Meta-Analysis of Case-Control Studies. Cancers (Basel) 2019; 11:cancers11081150. [PMID: 31405171 PMCID: PMC6721817 DOI: 10.3390/cancers11081150] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
A number of case-control studies regarding the association of the polymorphisms in the programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) genes with the risk of cancer have yielded inconsistent findings. Therefore, we have conducted a comprehensive, updated meta-analysis study to identify the impact of PD-1 and PD-L1 polymorphisms on overall cancer susceptibility. The findings revealed that PD-1 rs2227981 and rs11568821 polymorphisms significantly decreased the overall cancer risk (Odds Ratio (OR) = 0.82, 95% CI = 0.68–0.99, p = 0.04, TT vs. CT+CC; OR = 0.79, 95% CI = 0.67–0.94, p = 0.006, AG vs. GG, and OR = 0.82, 95% CI = 0.70–0.96, p = 0.020, AG+AA vs. GG, respectively), while PD-1 rs7421861 polymorphism significantly increased the risk of developing cancer (OR = 1.16, 95% CI = 1.02–1.33, p = 0.03, CT vs. TT). The PD-L1 rs4143815 variant significantly decreased the risk of cancer in homozygous (OR = 0.62, 95% CI = 0.41–0.94, p = 0.02), dominant (OR = 0.70, 95% CI = 0.50–0.97, p = 0.03), recessive (OR = 0.76, 95% CI = 0.60–0.96, p = 0.02), and allele (OR = 0.78, 95% CI = 0.63–0.96, p = 0.02) genetic models. No significant association between rs2227982, rs36084323, rs10204525, and rs2890658 polymorphisms and overall cancer risk has been found. In conclusions, the results of this meta-analysis have revealed an association between PD-1 rs2227981, rs11568821, rs7421861, as well as PD-L1 rs4143815 polymorphisms and overall cancer susceptibility.
Collapse
Affiliation(s)
- Mohammad Hashemi
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan 9816743463, Iran.
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran.
| | - Shima Karami
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran
| | - Sahel Sarabandi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 9816743175, Iran
| | - Abdolkarim Moazeni-Roodi
- Department of Clinical Biochemistry, Iranshahr University of Medical Sciences, Iranshahr 9916643535, Iran
| | - Andrzej Małecki
- Instititute of Physiotherapy and Health Sciences, The Jerzy Kukuczka Academy of Physical Education in Katowice, 40-065 Katowice, Poland
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, University of Manitoba, Winnipeg, MB R3E 3P5, Canada.
| | - Emilia Wiechec
- Department of Clinical and Experimental Medicine, Linköping University, 58183 Linköping, Sweden.
| |
Collapse
|
27
|
Computational Analysis of Protein Structure Changes as a Result of Nondeletion Insertion Mutations in Human β-Globin Gene Suggests Possible Cause of β-Thalassemia. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9210841. [PMID: 31275994 PMCID: PMC6582885 DOI: 10.1155/2019/9210841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 02/28/2019] [Accepted: 04/11/2019] [Indexed: 01/30/2023]
Abstract
Beta-thalassemia is described as a group of hereditary blood disorders characterized by abnormalities in the synthesis of beta chains of hemoglobin. These anomalies result in different phenotypes ranging from moderate to severe clinical symptoms to no symptoms at all. Most of the defects in hemoglobin arise directly from the mutations in the structural β-globin gene (HBB). Recent advances in computational tools have allowed the study of the relationship between the genotype and phenotype in many diseases including β-thalassemia. Due to high prevalence of β-thalassemia, these analyses have helped to understand the molecular basis of the disease in a better way. In this direction, a relational database, named HbVar, was developed in 2001 by a collective academic effort to provide quality and up-to-date information on the genomic variations leading to hemoglobinopathies and thalassemia. The database recorded details about each variant including the altered sequence, hematological defects, its pathology, and its occurrence along with references. In the present study, an attempt was made to investigate nondeletion mutations in the HBB picked up from HbVar and their effects using the in silico approach. Our study investigated 12 nucleotides insertion mutations in six different altered sequences. These 12 extra nucleotides led to the formation of a loop in the protein structure and did not alter its function. It appears that these mutations act as ‘silent' mutations. However, further in vitro studies are required to reach definitive conclusions.
Collapse
|
28
|
Ebbert MTW, Jensen TD, Jansen-West K, Sens JP, Reddy JS, Ridge PG, Kauwe JSK, Belzil V, Pregent L, Carrasquillo MM, Keene D, Larson E, Crane P, Asmann YW, Ertekin-Taner N, Younkin SG, Ross OA, Rademakers R, Petrucelli L, Fryer JD. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. Genome Biol 2019; 20:97. [PMID: 31104630 PMCID: PMC6526621 DOI: 10.1186/s13059-019-1707-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/06/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads that we call dark by depth, and others that have ambiguous alignment, called camouflaged. We assess how well long-read or linked-read technologies resolve these regions. RESULTS Based on standard whole-genome Illumina sequencing data, we identify 36,794 dark regions in 6054 gene bodies from pathways important to human health, development, and reproduction. Of these gene bodies, 8.7% are completely dark and 35.2% are ≥ 5% dark. We identify dark regions that are present in protein-coding exons across 748 genes. Linked-read or long-read sequencing technologies from 10x Genomics, PacBio, and Oxford Nanopore Technologies reduce dark protein-coding regions to approximately 50.5%, 35.6%, and 9.6%, respectively. We present an algorithm to resolve most camouflaged regions and apply it to the Alzheimer's Disease Sequencing Project. We rescue a rare ten-nucleotide frameshift deletion in CR1, a top Alzheimer's disease gene, found in disease cases but not in controls. CONCLUSIONS While we could not formally assess the association of the CR1 frameshift mutation with Alzheimer's disease due to insufficient sample-size, we believe it merits investigating in a larger cohort. There remain thousands of potentially important genomic regions overlooked by short-read sequencing that are largely resolved by long-read technologies.
Collapse
Affiliation(s)
- Mark T. W. Ebbert
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
| | - Tanner D. Jensen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Jonathon P. Sens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Joseph S. Reddy
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Perry G. Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602 USA
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602 USA
| | - Veronique Belzil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Luc Pregent
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA 98195 USA
| | - Eric Larson
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Paul Crane
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Yan W. Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224 USA
| | | | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
| | - John D. Fryer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224 USA
- Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL 32224 USA
| |
Collapse
|
29
|
Nguyen HH, Ma TTH, Vu NP, Bach QTN, Vu TH, Nguyen TD, Nong HV. Single nucleotide and structural variants of CYP2D6 gene in Kinh Vietnamese population. Medicine (Baltimore) 2019; 98:e15891. [PMID: 31145348 PMCID: PMC6709254 DOI: 10.1097/md.0000000000015891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/19/2019] [Accepted: 04/30/2019] [Indexed: 12/29/2022] Open
Abstract
CYP2D6 genetic variations could result in alteration of CYP2D6 enzyme activity, leading to dissimilarity among individuals in regard of drug metabolism.This study aims to detect all genetic variants, allele, and genotype frequencies of CYP2D6 gene in 136 unrelated healthy Kinh Vietnamese volunteers. All single nucleotide variants (SNVs) and structural variations (SVs) of CYP2D6 gene were identified by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) assay.Totally, 30 SNVs and 9 SVs including a whole gene deletion, 8 hybrid structures, and tandem arrangements were identified. Of the 7 novel SNVs detected, the 3157G>T (R329L) substitution was predicted to be deleterious by PROVEAN; the 3851G>A (W358X) variant resulted in a truncated protein; and the 2988G>A variant located in the intron 6 was predicted to be capable of modifying splicing motif by Human Splicing Finder. We determined 29 different genotypes of CYP2D6 from 136 individuals. The most common alleles were the CYP2D6*10 (43.75%), *1 (18.75%), and tandem arrangement *36-*10 (12.13%).This study provides best information on CYP2D6 polymorphism comprising the newly discovered SNVs, structural variations, and their frequencies in Kinh Vietnamese. These new data would be valuable in view of precise dosing of CYP2D6 metabolized drugs and giving better treatment outcome.
Collapse
Affiliation(s)
- Ha Hai Nguyen
- Institute of Genome Research
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi
| | | | - Nhung Phuong Vu
- Institute of Genome Research
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi
| | | | | | - Ton Dang Nguyen
- Institute of Genome Research
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi
| | - Hai Van Nong
- Institute of Genome Research
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi
| |
Collapse
|
30
|
Chen HI, Jagadeesh KA, Birgmeier J, Wenger AM, Guturu H, Schelley S, Bernstein JA, Bejerano G. An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease. Eur J Hum Genet 2018; 26:1810-1818. [PMID: 30087448 PMCID: PMC6244090 DOI: 10.1038/s41431-018-0221-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/09/2018] [Accepted: 06/26/2018] [Indexed: 12/16/2022] Open
Abstract
Approximately 2% of the human genome accounts for protein-coding genes, yet most known Mendelian disease-causing variants lie in exons or splice sites. Individuals who symptomatically present with monogenic disorders but do not possess function-altering variants in the protein-coding regions of causative genes may harbor variants in the surrounding gene regulatory domains. We present such a case: a male of Afghani descent was clinically diagnosed with Wilson Disease-a disorder of systemic copper buildup-but was found to have no function-altering coding variants in ATP7B (ENST00000242839.4), the typically causative gene. Our analysis revealed the homozygous variant chr13:g.52,586,149T>C (NC_000013.10, hg19) 676 bp into the ATP7B promoter, which disrupts a metal regulatory transcription factor 1 (MTF1) binding site and diminishes expression of ATP7B in response to copper intake, likely resulting in Wilson Disease. Our approach to identify the causative variant can be generalized to systematically discover function-altering non-coding variants underlying disease and motivates evaluation of gene regulatory variants.
Collapse
Affiliation(s)
- Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karthik A Jagadeesh
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
| | - Johannes Birgmeier
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
| | - Aaron M Wenger
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Harendra Guturu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Schelley
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
31
|
Da LS, Zhang Y, Zhang CJ, Bu LJ, Zhu YZ, Ma T, Gu KS. The PD-1 rs36084323 A > G polymorphism decrease cancer risk in Asian: A meta-analysis. Pathol Res Pract 2018; 214:1758-1764. [PMID: 30249505 DOI: 10.1016/j.prp.2018.09.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/30/2018] [Accepted: 09/14/2018] [Indexed: 12/11/2022]
Abstract
The rs36084323 A > G polymorphism in programmed cell death-1(PD-1) gene has been reported to be associated with cancer risk. However, the results of previous studies were inconsistent. Therefore, we performed a meta-analysis to identify the potential association, by searching the PubMed, EMBASE, Cochrane Library, and the Chinese CNKI, WANFANG and CBM databases. Data were extracted and odds ratios (ORs) with 95% confidence intervals (CIs) were estimated to assess the strength of the association. A total of 10 relevant studies involving 4445 cancer cases and 5126 controls were recruited. Overall, the results indicated that the PD-1 rs36084323 A > G polymorphism was not statistically associated with cancer risk. However, stratified analysis revealed that there was a statistically reduced cancer risk in Asians(G vs. A, OR = 0.89, 95%CI:0.81-0.97, P = 0.008, I2 = 48.8%; GG vs. AA, OR = 0.79, 95% CI:0.66-0.94, P = 0.008, I2 = 48.7%; GG/AG vs. AA, OR = 0.87, 95%CI:0.76-0.98, P = 0.017, I2 = 34.9%; GG vs. AG/AA, OR = 0.85, 95%CI:0.75-0.97, P = 0.027, I2 = 40%) and in the patients with EOC(AG vs. AA, OR = 0.69, 95%CI:0.54-0.90, P = 0.005, I2 = 0%; GG/AG vs. AA, OR = 0.67, 95%CI:0.52-0.85, P = 0.001, I2 = 0). Meta-regression showed that ethnicity (P = 0.029) but not cancer types (P = 0.792), source of controls (P = 0.207) or ample size (P = 0.585) were the sources of heterogeneity. This meta-analysis demonstrates the PD-1 rs36084323 A > G polymorphism is associated with decreased cancer risk in Asian, and suggests it could potentially serve as a biomarker to screen high-risk individuals. Large-scale and well-designed case-control studies are needed to enrich the evidence of this result.
Collapse
Affiliation(s)
- Liang-Shan Da
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Ying Zhang
- Department of Ultrasound, Affiliated Provincial Hospital of Anhui Medical University, Hefei 230001, China
| | - Cong-Jun Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Li-Jia Bu
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Yan-Zhe Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Tai Ma
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China.
| | - Kang-Sheng Gu
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China.
| |
Collapse
|
32
|
Promoter Variant Alters Expression of the Autophagic BECN1 Gene: Implications for Clinical Manifestations of Machado-Joseph Disease. THE CEREBELLUM 2018; 16:957-963. [PMID: 28699106 DOI: 10.1007/s12311-017-0875-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Autophagy is especially important in disorders where accumulation of the mutant protein is a hallmark, such as the Machado-Joseph disease/spinocerebellar ataxia type 3 (MJD/SCA3). We analyzed the promoter of the BECN1 gene, whose overexpression has been reported to exert neuroprotective effects in MJD, with the aim of finding variants that could be associated with expression levels of beclin-1 and could be tested as modifiers of onset and disease severity. A fragment encompassing the BECN1 promoter was sequenced in 95 MJD subjects and 120 controls. The impact of the variation detected on transcription factors (TFs) binding affinity was evaluated in silico and inferences concerning levels of expression were confirmed by fluorescence-based quantitative real-time PCR in a subset of 28 MJD subjects and 26 controls. Four previously described (rs60221525, rs116943570, rs34882610, and rs34037822) and one novel (c.-933delG) variants were identified. In silico analysis performed for the most frequent variants-rs60221525 C allele and rs116943570 T allele-predicted an impact of the presence of these alleles on TF binding affinity. BECN1 expression levels were in agreement with the in silico predictions, showing a tendency for decreased levels in samples with the rs60221525 C allele and for increased levels in samples with the rs116943570 T allele. MJD patients carrying the rs60221525 C allele presented a tendency for earlier estimated age at onset. Moreover, patients with the rs60221525 C allele presented a more severe clinical picture, compared to patients without this allele. The analysis of a larger number of patients from different cohorts, currently unavailable, would be required to confirm these results.
Collapse
|
33
|
Tang W, Chen S, Chen Y, Lin J, Lin J, Wang Y, Liu C, Kang M. Programmed death-1 polymorphisms is associated with risk of esophagogastric junction adenocarcinoma in the Chinese Han population: A case-control study involving 2,740 subjects. Oncotarget 2018; 8:39198-39208. [PMID: 28487496 PMCID: PMC5503606 DOI: 10.18632/oncotarget.17338] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/12/2017] [Indexed: 12/02/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) in Programmed cell death 1 (PD-1) gene may contribute to the development of cancer. In this study, we selected PD-1 rs10204525 T>C, rs2227982 A>G, rs36084323 T>C and rs7421861 A>G polymorphisms and designed a hospital-based case-control study to determine the potential relationship between these functional SNPs in PD-1 gene and esophagogastric junction adenocarcinoma (EGJA) risk. A total of 1,063 EGJA patients and 1,677 controls were enrolled from Eastern Chinese Han population. SNPscanTMgenotyping assay was used to analyze the genotyping of PD-1 polymorphisms. We found that PD-1 rs7421861 A>G polymorphism was associated with the development of EGJA. However, PD-1 rs2227982 A>G polymorphism was a protective factor for EGJA. In addition, PD-1 rs36084323 CC homozygote genotype might be associated with a borderline decreased risk of EGJA. In a subgroup analysis, a decreased risk of EGJA in never drinking and never smoking groups was identified. Haplotype comparison analysis suggested that PD-1 Trs10204525Grs2227982C36084323Ars7421861 haplotype significantly decreased the risk of EGJA. However, Trs10204525Grs2227982C36084323Grs7421861 haplotype in PD-1 gene may confer risk to EGJA. In conclusion, our study highlights rs2227982 A>G, rs36084323 T>C and rs7421861 A>G polymorphisms and haplotypes in PD-1 gene, especially within the intron region, are significantly associated with the risk of EGJA. Further case-control studies with larger sample size and detailed gene-environmental data to replicate these findings in different populations are needed to validate our conclusion.
Collapse
Affiliation(s)
- Weifeng Tang
- Department of Thoracic Surgery, The Union Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Shuchen Chen
- Department of Thoracic Surgery, The Union Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yu Chen
- Department of Medical Oncology, Fujian Provincial Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province, China
| | - Jihong Lin
- Department of Thoracic Surgery, The Union Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jiangbo Lin
- Department of Thoracic Surgery, The Union Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, China
| | - Yafeng Wang
- Department of Cardiology, The People's Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, Yunnan Province, China
| | - Chao Liu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, The Union Clinical Medical College of Fujian Medical University, Fuzhou, Fujian Province, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian Province, China.,Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, Fujian Province, China
| |
Collapse
|
34
|
Gambichler T, Mahjurian-Namari M, Reininghaus L, Schmitz L, Skrygan M, Schulze HJ, Schaller J, Girolomoni G. Lysyl oxidase-like-2 mutations and reduced mRNA and protein expression in mid-dermal elastolysis. Clin Exp Dermatol 2018; 44:47-51. [PMID: 29845638 DOI: 10.1111/ced.13652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2017] [Indexed: 01/26/2023]
Abstract
BACKGROUND Mid-dermal elastolysis (MDE) is a rare skin condition, characterized by selective loss of elastic fibres in the mid dermis. The pathogenesis of MDE is still unclear. AIM To investigate expression of lysyl oxidase-like 2 (LOXL2) in a reasonable sample of patients with MDE and to search for mutations in LOXL2. METHODS We investigated archived lesional tissue of 13 patients with MDE and skin tissue samples of 10 sex- and age-matched healthy controls (HCs). Gene and protein expression of LOXL2 was investigated using real-time reverse-transcription PCR and immunohistochemistry. Mutation analysis was performed using the Sanger method. RESULTS We observed decreased LOXL2 mRNA expression in lesional skin of patients with MDE (0.48 ± 0.16) compared with healthy skin of the same patients (1.5 ± 0.51) and normal skin of HCs (1.9 ± 0.13). Compared with healthy patient skin (epidermis 2.38 ± 1.6, dermis 1.2 ± 1), LOXL2 protein expression in lesional patient skin (epidermis 1.1 ± 0.7, dermis 0.3 ± 0.45) was significantly decreased (P < 0.04 and P = 0.02, respectively). Mutation analysis of the entire LOXL2 gene could be performed for five patients, all of whom were found to have at least one mutation in the LOXL2 gene. Three of these had a mutation in the promoter region (c.967 G>C, c.1022 C>T, and c.1025 G>A, respectively), and one of them also had a mutation in the splice region of intron 11/exon 12 (IVS11-1 G>A). Of the remaining two patients, one had a mutation in exon 3 (T1391), and the other had a mutation in exon 11 (C663Y). CONCLUSIONS Our present data suggest that decreased elastin renewal due to LOXL2 mutations and consecutive reduced LOXL2 expression contribute to the pathogenesis of MDE.
Collapse
Affiliation(s)
- T Gambichler
- Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | | | - L Reininghaus
- Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - L Schmitz
- Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - M Skrygan
- Department of Dermatology, Ruhr-University Bochum, Bochum, Germany
| | - H-J Schulze
- Fachklinik Hornheide, Department of Dermatology and Dermato-Histo-Pathology, Münster, Germany
| | - J Schaller
- Dermatopathology Duisburg, Duisburg, Germany
| | - G Girolomoni
- Section of Dermatology and Venereology, Department of Medicine, University of Verona, Verona, Italy
| |
Collapse
|
35
|
Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Infante M, Durán M, Marcos G, Lastra E, Gómez-Barrero S, Velasco EA. Genetic dissection of the BRCA2 promoter and transcriptional impact of DNA variants. Breast Cancer Res Treat 2018; 171:53-63. [PMID: 29766361 DOI: 10.1007/s10549-018-4826-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/16/2018] [Indexed: 11/28/2022]
Abstract
PURPOSE Promoter mutations may affect transcription and can be associated with human diseases. However, the promoters of the breast cancer (BC) genes are not regularly screened. Our goal was to investigate the BRCA2 promoter in order to study a possible correlation between impaired transcription and disease. METHODS The proximal and core promoter of the BRCA2 gene was sequenced in 95 high-risk BC patients. A BRCA2-promoter insert [- 938 to + 312 from the transcription start site (TSS)] was generated and cloned into the firefly luciferase vector pGL4.10. Promoter variants and deletions were introduced by site-directed mutagenesis and quantified by Dual-Luciferase assays and semi-quantitative RT-PCR. RESULTS Three different variants were detected in high-risk BC patients: rs3092989, rs206118, and rs563971900. Functional mapping of 13 overlapping deletions revealed four down-regulating segments (TSS positions): -59_-10del/µdel3 (16% of activity of the wild-type construct), -104_-55del/µdel4 (62%), -239_-190del/µdel7 (39%), -464_-415/µdel12 (78%), suggesting the presence therein of putative transcriptional activator motifs. Additionally, six microdeletions rendered luciferase overexpression: +32_+81del/µdel1 (356%), -14_+36del/µdel2 (180%), -194_-145del/µdel6 (154%), -284_-235del/µdel8 (168%), -329_-280del/µdel9 (111%), and -509_-460del/µdel13 (139%), which is indicative of repressor elements. Functional assays of 15 promoter variants (including those detected in patients) showed that ten of them significantly altered expression with seven up-regulating (113-163%) and three down-regulating (rs551887850_G, rs570548398_T, rs55880202_T; 72-83%) SNPs. Eight of them were located in an ENCODE-DNase Hypersensitive Cluster (TSS - 185 to + 105) where most active transcriptional motifs are known to be placed. CONCLUSIONS BRCA2 expression is highly sensitive to promoter variations as most of them induced relevant changes. Moreover, we mapped critical regions of the BRCA2 promoter that may constitute potential targets for regulatory variants. Three SNPs moderately decreased luciferase activity, but confirmation of its potential pathogenicity requires further analysis. These data reinforce the need to screen the promoter regions of breast cancer genes with a view to discovering novel deleterious mutations.
Collapse
Affiliation(s)
- Eugenia Fraile-Bethencourt
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Beatriz Díez-Gómez
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (UVa-CSIC), Valladolid, Spain
| | - Mercedes Durán
- Cancer Genetics, Instituto de Biología y Genética Molecular (UVa-CSIC), Valladolid, Spain
| | - Germán Marcos
- Servicio de Oncología, Hospital Río Hortega, Valladolid, Spain
| | - Enrique Lastra
- Servicio de Oncología, Hospital Universitario de Burgos, Burgos, Spain
| | | | - Eladio A Velasco
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain.
| |
Collapse
|
36
|
Li Y, Bao C, Gu S, Ye D, Jing F, Fan C, Jin M, Chen K. Associations between novel genetic variants in the promoter region of MALAT1 and risk of colorectal cancer. Oncotarget 2017; 8:92604-92614. [PMID: 29190941 PMCID: PMC5696207 DOI: 10.18632/oncotarget.21507] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/29/2017] [Indexed: 12/19/2022] Open
Abstract
The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a well-known long non-coding RNA, is involved in pathogenesis and progress of multiple tumors. However, no study has been performed to investigate the relationship between the genetic variants in promoter region of MALAT1 and colorectal cancer risk. In this study, we conducted a two-stage case-control study to evaluate whether MALAT1 genetic variants were associated with colorectal cancer risk. We identified that a single nucleotide polymorphism (SNP) rs1194338 was significantly associated with the decreased colorectal cancer risk with an odds ratio (OR) of 0.70 [95% confidence interval (CI) = 0.49-0.99] in the combined stage. The subsequently stratified analyses showed that the protective effect of rs1194338 was more pronounced in several subgroups. Furthermore, gene expression profiling analysis revealed overexpression of MALAT1 mRNA in colorectal cancer tissue compared with normal controls. Confirmation studies with large sample size and further mechanistic investigations into the function of MALAT1 and its genetic variants are warranted to advance our understanding of their roles in colorectal carcinogenesis, and to aid in the development of novel and targeted therapeutic strategies.
Collapse
Affiliation(s)
- Yingjun Li
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, China.,Department of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Chengzhen Bao
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Simeng Gu
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Ding Ye
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Fangyuan Jing
- Department of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Chunhong Fan
- Department of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Mingjuan Jin
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Kun Chen
- Department of Epidemiology and Health Statistics, Zhejiang University School of Public Health, Hangzhou, China
| |
Collapse
|
37
|
Sundralingam T, Tennekoon KH, de Silva S, De Silva S, Hewage AS. Pathogenic and likely pathogenic genetic alterations and polymorphisms in growth hormone gene (GH1) and growth hormone releasing hormone receptor gene (GHRHR) in a cohort of isolated growth hormone deficient (IGHD) children in Sri Lanka. Growth Horm IGF Res 2017; 36:22-29. [PMID: 28910730 DOI: 10.1016/j.ghir.2017.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Genetic alterations in GH1 and GHRHR genes are known to cause isolated growth hormone deficiency (IGHD). Of these, GHRHR codon 72 mutation has been reported to be highly prevalent in the Indian subcontinent, but among Sri Lankans its prevalence was low compared to reports from neighboring countries. The present study was therefore carried out to identify genetic alterations in the GH1 gene and rest of the GHRHR gene in a cohort of Sri Lankan IGHD patients who tested negative for GHRHR codon 72 mutation. METHODS Fifty five IGHD children negative for codon 72 (GHRHR) mutation were screened for gross GH1 gene deletion by polymerase chain reaction (PCR) and restriction fragment length polymorphism technique. The coding, intronic and promoter regions of the GH1 gene were sequenced in children who were negative for GH1 deletion (N=53). In a subset (N=40), coding, flanking intronic and promoter regions of the GHRHR gene were screened by single strand conformation polymorphism/sequencing. Identified coding region and intronic variants were subjected to in silico analysis to ascertain pathogenicity. Family members available were screened for the significant variants observed in the index child. RESULTS Gross GH1 gene deletions, 6.7kb and 7.0kb were observed in one child each. One novel and 24 reported single nucleotide variants (SNVs) were observed in the GH1 gene and its promoter. These included one reported pathogenic splice site mutation (c.172-2A>T) and one reported likely pathogenic missense mutation (c.406G>T). One large novel deletion of 5875 base pairs that included exon 1, one likely pathogenic novel SNV (c.211G>T) and 18 reported SNVs were observed in the GHRHR gene. Fourteen variants observed were of uncertain significance (8 in GH1 and 6 in GHRHR), twenty three variants were likely benign (11 in GH1 and 12 in GHRHR) and four variants were benign (4 in GH1 and none in GHRHR). CONCLUSION In a cohort of IGHD children, six pathogenic or likely pathogenic genetic alterations of either GH1 gene or GHRHR gene were found. These affected a total of six children. Pathogenic status of four of these had been reported in the literature. Novel SNV in the GHRHR gene was predicted to be pathogenic through in silico analysis. The large novel deletion is likely to be pathogenic as it included exon 1 of GHRHR gene. Analysis of other genes will be needed to ascertain the genetic cause of IGHD in the remaining children.
Collapse
Affiliation(s)
- Tharmini Sundralingam
- Institute of Biochemistry, Molecular Biology and Biotechnology, 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Shamya de Silva
- Department of Paediatrics, Faculty of Medicine, PO Box 271, Kynsey Road, Colombo 08, Sri Lanka; Lady Ridgeway Hospital, Dr. Danister de Silva Mawatha, Colombo 08, Sri Lanka
| | - Sumadee De Silva
- Institute of Biochemistry, Molecular Biology and Biotechnology, 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Asanka Sudeshini Hewage
- Institute of Biochemistry, Molecular Biology and Biotechnology, 90, Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| |
Collapse
|
38
|
Zou Y, Zhang Z, Liu Y, Liu D, Xu W. Are programmed cell death 1 gene polymorphisms correlated with susceptibility to rheumatoid arthritis?: A meta-analysis. Medicine (Baltimore) 2017; 96:e7805. [PMID: 28858091 PMCID: PMC5585485 DOI: 10.1097/md.0000000000007805] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Several studies investigated the relationship between programmed cell death 1 (PDCD1) gene polymorphisms and rheumatoid arthritis (RA) risk, but the results were controversial. To explore whether PDCD1 gene polymorphisms have an effect on RA risk, we conducted this meta-analysis to investigate the relationships between PDCD1 polymorphisms (rs36084323 [PD-1.1 G/A], rs11568821 [PD-1.3 G/A] and rs2227981 [PD-1.5 C/T]) and RA risk under 4 genetic models. METHODS PubMed, EMBASE, Web of Science, Cochrane Library China National Knowledge Infrastructure (CNKI), and Chinese Biomedical Literature Database (CBLM) were systematically searched for all eligible case-control studies. The last search was updated on September 10, 2016. Studies were accessed using Newcastle-Ottawa Scale case control study (NOS), and the combined effect size was calculated using STATA software, version 12.0. The pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to assess the association. Heterogeneity analysis and subgroup analysis were also performed. Sensitivity analysis and publication bias were also performed if necessary. RESULTS This meta-analysis included 6 studies. The result demonstrated null association between rs36084323 (PD-1.1 G/A) polymorphism and RA susceptibility in all 4 genetic models. With regard to rs11568821 (PD-1.3 G/A), statistically significant association with RA risk was observed under allele model in Caucasians (allele model A vs G, OR = 1.19, 95% CI = 1.03-1.41). There was no significant association between rs2227981 (PD-1.5 C/T) polymorphism and RA risk. CONCLUSION The present study suggests that mutant A allele in rs11568821 (PD-1.3 G/A) might increase the susceptibility to RA in Caucasians.
Collapse
Affiliation(s)
- Yuming Zou
- Department of Orthopedics, Changhai Hospital, The First Affiliated Hospital of the Second Military Medical University
| | - Ziteng Zhang
- Department of Health Toxicology, College of Tropical Medicine and Public Health, Second Military Medical University, Shanghai, China
| | - Yangang Liu
- Department of Health Toxicology, College of Tropical Medicine and Public Health, Second Military Medical University, Shanghai, China
| | - Denghui Liu
- Department of Orthopedics, Changhai Hospital, The First Affiliated Hospital of the Second Military Medical University
| | - Weidong Xu
- Department of Orthopedics, Changhai Hospital, The First Affiliated Hospital of the Second Military Medical University
| |
Collapse
|
39
|
Functional classification of DNA variants by hybrid minigenes: Identification of 30 spliceogenic variants of BRCA2 exons 17 and 18. PLoS Genet 2017; 13:e1006691. [PMID: 28339459 PMCID: PMC5384790 DOI: 10.1371/journal.pgen.1006691] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 04/07/2017] [Accepted: 03/14/2017] [Indexed: 11/30/2022] Open
Abstract
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants. A splicing reporter minigene with BRCA2 exons 14 to-20 (MGBR2_ex14-20) was constructed in the pSAD vector. Fifty-two candidate variants were selected with splicing prediction programs, introduced in MGBR2_ex14-20 by site-directed mutagenesis and assayed in triplicate in MCF-7 cells. Wild type MGBR2_ex14-20 produced a stable transcript of the expected size (1,806 nucleotides) and structure (V1-[BRCA2_exons_14–20]–V2). Functional mapping by microdeletions revealed essential sequences for exon recognition on the 3’ end of exon 17 (c.7944-7973) and the 5’ end of exon 18 (c.7979-7988, c.7999-8013). Thirty out of the 52 selected variants induced anomalous splicing in minigene assays with >16 different aberrant transcripts, where exon skipping was the most common event. A wide range of splicing motifs were affected including the canonical splice sites (15 variants), novel alternative sites (3 variants), the polypyrimidine tract (3 variants) and enhancers/silencers (9 variants). According to the guidelines of the American College of Medical Genetics and Genomics (ACMG), 20 variants could be classified as pathogenic (c.7806-2A>G, c.7806-1G>A, c.7806-1G>T, c.7806-1_7806-2dup, c.7976+1G>A, c.7977-3_7978del, c.7977-2A>T, c.7977-1G>T, c.7977-1G>C, c.8009C>A, c.8331+1G>T and c.8331+2T>C) or likely pathogenic (c.7806-9T>G, c.7976G>C, c.7976G>A, c.7977-7C>G, c.7985C>G, c.8023A>G, c.8035G>T and c.8331G>A), accounting for 30.8% of all pathogenic/likely pathogenic variants of exons 17–18 at the BRCA Share database. The remaining 8 variants (c.7975A>G, c.7977-6T>G, c.7988A>T, c.7992T>A, c.8007A>G, c.8009C>T, c.8009C>G, and c.8072C>T) induced partial splicing anomalies with important ratios of the full-length transcript (≥70%), so that they remained classified as VUS. Aberrant splicing is therefore especially prevalent in BRCA2 exons 17 and 18 due to the presence of active ESEs involved in exon recognition. Splicing functional assays with minigenes are a valuable strategy for the initial characterization of the splicing outcomes and the subsequent clinical interpretation of variants of any disease-gene, although these results should be checked, whenever possible, against patient RNA. A significant proportion of disease-causing mutations of inherited disorders impair splicing. Massive sequencing projects of genetic diseases generate thousands of sequence variations that require functional and clinical interpretations. We have shown that splicing reporter minigenes of the breast cancer genes BRCA1 and BRCA2 are useful tools to functionally test DNA variants. In this work, we have constructed a 7-exon BRCA2 minigene (exons 14 to 20) where we mapped critical splicing regulatory sequences and tested 52 selected variants of exons 17 and 18 detected in breast cancer patients. We finely located three DNA segments on both exons that presumably contain splicing enhancer sequences. We observed that a total of 30 variants of any type disrupted the splicing patterns and, given the severity of their outcomes, we classified 20 of them as pathogenic or likely pathogenic. We also showed that a wide range of splicing elements were affected including canonical and novel 5’ and 3’ splice sites, the polypyrimidine tract and enhancer and silencer sequences. We concluded that splicing aberrations are frequent in Hereditary Breast and Ovarian Cancer and that minigenes are valuable tools to functionally classify DNA variants of any human disease gene under the splicing viewpoint.
Collapse
|
40
|
Radziwon A, Arno G, K Wheaton D, McDonagh EM, Baple EL, Webb-Jones K, G Birch D, Webster AR, MacDonald IM. Single-base substitutions in the CHM promoter as a cause of choroideremia. Hum Mutat 2017; 38:704-715. [PMID: 28271586 DOI: 10.1002/humu.23212] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 02/13/2017] [Accepted: 02/25/2017] [Indexed: 12/18/2022]
Abstract
Although over 150 unique mutations affecting the coding sequence of CHM have been identified in patients with the X-linked chorioretinal disease choroideremia (CHM), no regulatory mutations have been reported, and indeed the promoter has not been defined. Here, we describe two independent families affected by CHM bearing a mutation outside the gene's coding region at position c.-98: C>A and C>T, which segregated with the disease. The male proband of family 1 was found to lack CHM mRNA and its gene product Rab escort protein 1, whereas whole-genome sequencing of an affected male in family 2 excluded the involvement of any other known retinal genes. Both mutations abrogated luciferase activity when inserted into a reporter construct, and by further employing the luciferase reporter system to assay sequences 5' to the gene, we identified the CHM promoter as the region encompassing nucleotides c.-119 to c.-76. These findings suggest that the CHM promoter region should be examined in patients with CHM who lack coding sequence mutations, and reveals, for the first time, features of the gene's regulation.
Collapse
Affiliation(s)
- Alina Radziwon
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, Canada
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital, London, UK
| | | | | | - Emma L Baple
- Genomics England, Queen Mary University of London, London, UK.,Medical Research (Level 4), RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
| | | | | | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital, London, UK
| | - Ian M MacDonald
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, Canada
| |
Collapse
|
41
|
Liu Q, Thompson BA, Ward RL, Hesson LB, Sloane MA. Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome. Hum Mutat 2016; 37:417-26. [DOI: 10.1002/humu.22971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 02/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Qing Liu
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Bryony A. Thompson
- Huntsman Cancer Institute; University of Utah; Salt Lake City Utah
- Centre for Epidemiology and Biostatistics; Melbourne School of Population and Global Health; University of Melbourne; Melbourne Victoria Australia
| | - Robyn L. Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
- Level 3 Brian Wilson Chancellery; The University of Queensland; Brisbane Queensland Australia
| | - Luke B. Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Mathew A. Sloane
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| |
Collapse
|
42
|
Davidson A, Liskova P, Evans C, Dudakova L, Nosková L, Pontikos N, Hartmannová H, Hodaňová K, Stránecký V, Kozmík Z, Levis H, Idigo N, Sasai N, Maher G, Bellingham J, Veli N, Ebenezer N, Cheetham M, Daniels J, Thaung C, Jirsova K, Plagnol V, Filipec M, Kmoch S, Tuft S, Hardcastle A. Autosomal-Dominant Corneal Endothelial Dystrophies CHED1 and PPCD1 Are Allelic Disorders Caused by Non-coding Mutations in the Promoter of OVOL2. Am J Hum Genet 2016; 98:75-89. [PMID: 26749309 PMCID: PMC4716680 DOI: 10.1016/j.ajhg.2015.11.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/13/2015] [Indexed: 11/27/2022] Open
Abstract
Congenital hereditary endothelial dystrophy 1 (CHED1) and posterior polymorphous corneal dystrophy 1 (PPCD1) are autosomal-dominant corneal endothelial dystrophies that have been genetically mapped to overlapping loci on the short arm of chromosome 20. We combined genetic and genomic approaches to identify the cause of disease in extensive pedigrees comprising over 100 affected individuals. After exclusion of pathogenic coding, splice-site, and copy-number variations, a parallel approach using targeted and whole-genome sequencing facilitated the identification of pathogenic variants in a conserved region of the OVOL2 proximal promoter sequence in the index families (c.−339_361dup for CHED1 and c.−370T>C for PPCD1). Direct sequencing of the OVOL2 promoter in other unrelated affected individuals identified two additional mutations within the conserved proximal promoter sequence (c.−274T>G and c.−307T>C). OVOL2 encodes ovo-like zinc finger 2, a C2H2 zinc-finger transcription factor that regulates mesenchymal-to-epithelial transition and acts as a direct transcriptional repressor of the established PPCD-associated gene ZEB1. Interestingly, we did not detect OVOL2 expression in the normal corneal endothelium. Our in vitro data demonstrate that all four mutated OVOL2 promoters exhibited more transcriptional activity than the corresponding wild-type promoter, and we postulate that the mutations identified create cryptic cis-acting regulatory sequence binding sites that drive aberrant OVOL2 expression during endothelial cell development. Our data establish CHED1 and PPCD1 as allelic conditions and show that CHED1 represents the extreme of what can be considered a disease spectrum. They also implicate transcriptional dysregulation of OVOL2 as a common cause of dominantly inherited corneal endothelial dystrophies.
Collapse
|
43
|
Molecular and cellular analysis of three novel alpha2-globin gene promoter mutations [HBA2: c.-59C>T], [HBA2: c.-81C>A] and [HBA2: c.-91G>A] reveal varying patterns of transcriptional and translational activities. Pathology 2015; 46:46-52. [PMID: 24300714 DOI: 10.1097/pat.0000000000000023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
While point mutations affecting the promoter region of β-globin gene are widely described, there are no well characterised reports of any point mutations currently found in the promoter of the α2-globin (HBA2) gene. We present clinical and experimental data for three novel HBA2 gene core and proximal promoter mutations. Using an in vitro system designed to assess the impact of point mutations, the three novel [HBA2:c.-59C>T], [HBA2:c.-81C>A] and [HBA2:c.-91G>A] promoter mutations identified in three unrelated patients were analysed for HBA2 gene transcriptional and translational activities. Following the generation and transfection of expression vectors carrying each mutation, the HBA2 transcription activity of the promoters from each mutant was analysed with quantitative real time-PCR (qReTi-PCR) technique. Immunofluorochemistry (IFC) was used to analyse HBA2 protein synthesis. The analyses showed that [HBA2:c.-59C>T] and [HBA2:c.-91G>A] mutant constructs caused significant reduction in the HBA2 transcription levels by 53.7% (p = 0.0008) and 36.2% (p = 0.004), respectively, resulting in markedly lower HBA2 protein labelling when compared to the wild type as shown with subsequent IFC analysis. Conversely, the [HBA2:c.-81C>A] construct showed no significant changes in either transcription (p = 0.089) or in protein labelling when compared to the wild type. The equal pAmp transcription levels found in each group confirmed that the observed labelling differences were not due to varying transfection efficiencies. This study emphasises the importance of in vitro studies to establish the impact of base substitutions on the level of gene expression, and the value of these studies in clinicopathological correlation so that appropriate advice can be given in genetic counselling.
Collapse
|
44
|
Li Z, Schonberg R, Guidugli L, Johnson AK, Arnovitz S, Yang S, Scafidi J, Summar ML, Vezina G, Das S, Chapman K, del Gaudio D. A novel mutation in the promoter of RARS2 causes pontocerebellar hypoplasia in two siblings. J Hum Genet 2015; 60:363-9. [PMID: 25809939 DOI: 10.1038/jhg.2015.31] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/09/2015] [Accepted: 02/26/2015] [Indexed: 02/04/2023]
Abstract
Pontocerebellar hypoplasia (PCH) is characterized by hypoplasia and atrophy of the cerebellum, variable pontine atrophy, microcephaly, severe mental and motor impairments and seizures. Mutations in 11 genes have been reported in 8 out of 10 forms of PCH. Recessive mutations in the mitochondrial arginyl-transfer RNA synthetase gene (RARS2) have been recently associated with PCH type 6, which is characterized by early-onset encephalopathy with signs of oxidative phosphorylation defect. Here we describe the clinical presentation, neuroimaging findings and molecular characterizations of two siblings with a clinical diagnosis of PCH who displayed a novel variant (c.-2A>G) in the 5'-UTR of the RARS2 gene in the homozygous state. This variant was identified through next-generation sequencing testing of a panel of nine genes known to be involved in PCH. Gene expression and functional studies demonstrated that the c.-2A>G sequence change directly leads to a reduced RARS2 messenger RNA expression in the patients by decreasing RARS2 promoter activity, thus providing evidence that mutations in the RARS2 promoter are likely to represent a new causal mechanism of PCH6.
Collapse
Affiliation(s)
- Zejuan Li
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Rhonda Schonberg
- 1] Division of Genetics and Metabolism, Children's National Health System, Washington, DC, USA [2] The George Washington University Medical Center, Washington, DC, USA
| | - Lucia Guidugli
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - Stephen Arnovitz
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sandra Yang
- Division of Genetics and Metabolism, Children's National Health System, Washington, DC, USA
| | - Joseph Scafidi
- 1] The George Washington University Medical Center, Washington, DC, USA [2] Division of Neurology, Children's National Health System, Washington, DC, USA
| | - Marshall L Summar
- 1] Division of Genetics and Metabolism, Children's National Health System, Washington, DC, USA [2] The George Washington University Medical Center, Washington, DC, USA
| | - Gilbert Vezina
- 1] The George Washington University Medical Center, Washington, DC, USA [2] Department of Radiology, Children's National Health System, Washington, DC, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Kimberly Chapman
- 1] Division of Genetics and Metabolism, Children's National Health System, Washington, DC, USA [2] The George Washington University Medical Center, Washington, DC, USA
| | | |
Collapse
|
45
|
SIX1 gene: absence of mutations in children with isolated congenital anomalies of kidney and urinary tract. J Nephrol 2014; 27:667-71. [DOI: 10.1007/s40620-014-0112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 05/13/2014] [Indexed: 11/30/2022]
|
46
|
Abstract
Genomic information reported as haplotypes rather than genotypes will be increasingly important for personalized medicine. Current technologies generate diploid sequence data that is rarely resolved into its constituent haplotypes. Furthermore, paradigms for thinking about genomic information are based on interpreting genotypes rather than haplotypes. Nevertheless, haplotypes have historically been useful in contexts ranging from population genetics to disease-gene mapping efforts. The main approaches for phasing genomic sequence data are molecular haplotyping, genetic haplotyping, and population-based inference. Long-read sequencing technologies are enabling longer molecular haplotypes, and decreases in the cost of whole-genome sequencing are enabling the sequencing of whole-chromosome genetic haplotypes. Hybrid approaches combining high-throughput short-read assembly with strategic approaches that enable physical or virtual binning of reads into haplotypes are enabling multi-gene haplotypes to be generated from single individuals. These techniques can be further combined with genetic and population approaches. Here, we review advances in whole-genome haplotyping approaches and discuss the importance of haplotypes for genomic medicine. Clinical applications include diagnosis by recognition of compound heterozygosity and by phasing regulatory variation to coding variation. Haplotypes, which are more specific than less complex variants such as single nucleotide variants, also have applications in prognostics and diagnostics, in the analysis of tumors, and in typing tissue for transplantation. Future advances will include technological innovations, the application of standard metrics for evaluating haplotype quality, and the development of databases that link haplotypes to disease.
Collapse
Affiliation(s)
- Gustavo Glusman
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
| | - Hannah C Cox
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
| | - Jared C Roach
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
| |
Collapse
|
47
|
Taube JR, Sperle K, Banser L, Seeman P, Cavan BCV, Garbern JY, Hobson GM. PMD patient mutations reveal a long-distance intronic interaction that regulates PLP1/DM20 alternative splicing. Hum Mol Genet 2014; 23:5464-78. [PMID: 24890387 DOI: 10.1093/hmg/ddu271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Alternative splicing of the proteolipid protein 1 gene (PLP1) produces two forms, PLP1 and DM20, due to alternative use of 5' splice sites with the same acceptor site in intron 3. The PLP1 form predominates in central nervous system RNA. Mutations that reduce the ratio of PLP1 to DM20, whether mutant or normal protein is formed, result in the X-linked leukodystrophy Pelizaeus-Merzbacher disease (PMD). We investigated the ability of sequences throughout PLP1 intron 3 to regulate alternative splicing using a splicing minigene construct transfected into the oligodendrocyte cell line, Oli-neu. Our data reveal that the alternative splice of PLP1 is regulated by a long-distance interaction between two highly conserved elements that are separated by 581 bases within the 1071-base intron 3. Further, our data suggest that a base-pairing secondary structure forms between these two elements, and we demonstrate that mutations of either element designed to destabilize the secondary structure decreased the PLP1/DM20 ratio, while swap mutations designed to restore the structure brought the PLP1/DM20 ratio to near normal levels. Sequence analysis of intron 3 in families with clinical symptoms of PMD who did not have coding-region mutations revealed mutations that segregated with disease in three families. We showed that these patient mutations, which potentially destabilize the secondary structure, also reduced the PLP1/DM20 ratio. This is the first report of patient mutations causing disease by disruption of a long-distance intronic interaction controlling alternative splicing. This finding has important implications for molecular diagnostics of PMD.
Collapse
Affiliation(s)
- Jennifer R Taube
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Karen Sperle
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Linda Banser
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Pavel Seeman
- Department of Child Neurology, DNA Laboratory, 2nd School of Medicine, Charles University and University Hospital Motol, 150 06 Prague 5, Czech Republic
| | | | - James Y Garbern
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Grace M Hobson
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA, Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA and Department of Pediatrics, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| |
Collapse
|
48
|
Funnell AP, Crossley M. Hemophilia B Leyden and once mysterious cis-regulatory mutations. Trends Genet 2014; 30:18-23. [DOI: 10.1016/j.tig.2013.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 09/18/2013] [Accepted: 09/20/2013] [Indexed: 11/28/2022]
|
49
|
Rose AM, Shah AZ, Waseem NH, Chakarova CF, Alfano G, Coussa RG, Ajlan R, Koenekoop RK, Bhattacharya SS. Expression of PRPF31 and TFPT: regulation in health and retinal disease. Hum Mol Genet 2012; 21:4126-37. [PMID: 22723017 DOI: 10.1093/hmg/dds242] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PRPF31, a gene located at chromosome 19q13.4, encodes the ubiquitous splicing factor PRPF31. The gene lies in a head-to-head arrangement with TFPT, a poorly characterized gene with a role in cellular apoptosis. Mutations in PRPF31 have been implicated in autosomal dominant retinitis pigmentosa (adRP), a frequent and important cause of blindness worldwide. Disease associated with PRPF31 mutations is unusual, in that there is often non-penetrance of the disease phenotype in affected families, caused by differential expression of PRPF31. This study aimed to characterize the basic promoter elements of PRPF31 and TFPT. Luciferase reporter constructs were made, using genomic DNA from an asymptomatic individual with a heterozygous deletion of the entire putative promoter region. Fragments were tested by the dual-luciferase reporter assay in HeLa and RPE-1 cell lines. A comparison was made between the promoter regions of symptomatic and asymptomatic mutation-carrying individuals. A patient (CAN493) with adRP was identified, harbouring a regulatory region mutation; both alleles were assayed by the dual-luciferase reporter assay. Luciferase assays led to the identification of core promoters for both PRPF31 and TFPT; despite their shared gene architecture, the two genes appear to be controlled by slightly different regulatory regions. One functional polymorphism was identified in the PRPF31 promoter that increased transcriptional activation. The change was not, however, consistent with the observed symptomatic-asymptomatic phenotypes in a family affected by PRPF31-adRP. Analysis of the mutant promoter fragment from CAN493 showed a >50% reduction in promoter activity, suggesting a disease mechanism of functional haploinsufficiency-the first report of this disease mechanism in adRP.
Collapse
Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London EC1V 9EL, UK.
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Cloning and ontogenetic expression of the uncoupling protein 1 gene UCP1 in sheep. J Appl Genet 2012; 53:203-12. [DOI: 10.1007/s13353-012-0086-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 01/26/2012] [Accepted: 01/26/2012] [Indexed: 12/19/2022]
|