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Leow KQ, Tonta MA, Lu J, Coleman HA, Parkington HC. Towards understanding sex differences in autism spectrum disorders. Brain Res 2024; 1833:148877. [PMID: 38513995 DOI: 10.1016/j.brainres.2024.148877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by social deficits, repetitive behaviours and lack of empathy. Its significant genetic heritability and potential comorbidities often lead to diagnostic and therapeutic challenges. This review addresses the biological basis of ASD, focusing on the sex differences in gene expression and hormonal influences. ASD is more commonly diagnosed in males at a ratio of 4:1, indicating a potential oversight in female-specific ASD research and a risk of underdiagnosis in females. We consider how ASD manifests differently across sexes by exploring differential gene expression in female and male brains and consider how variations in steroid hormones influence ASD characteristics. Synaptic function, including excitation/inhibition ratio imbalance, is influenced by gene mutations and this is explored as a key factor in the cognitive and behavioural manifestations of ASD. We also discuss the role of micro RNAs (miRNAs) and highlight a novel mutation in miRNA-873, which affects a suite of key synaptic genes, neurexin, neuroligin, SHANK and post-synaptic density proteins, implicated in the pathology of ASD. Our review suggests that genetic predisposition, sex differences in brain gene expression, and hormonal factors significantly contribute to the presentation, identification and severity of ASD, necessitating sex-specific considerations in diagnosis and treatments. These findings advocate for personalized interventions to improve the outcomes for individuals with ASD.
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Affiliation(s)
- Karen Q Leow
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia
| | - Mary A Tonta
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia
| | - Jing Lu
- Tianjin Institute of Infectious Disease, Second Hospital of Tianjin Medical University, China
| | - Harold A Coleman
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia
| | - Helena C Parkington
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia.
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2
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Janoski JR, Aiello I, Lundberg CW, Finkielstein CV. Circadian clock gene polymorphisms implicated in human pathologies. Trends Genet 2024:S0168-9525(24)00110-0. [PMID: 38871615 DOI: 10.1016/j.tig.2024.05.006] [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: 02/27/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
Circadian rhythms, ~24 h cycles of physiological and behavioral processes, can be synchronized by external signals (e.g., light) and persist even in their absence. Consequently, dysregulation of circadian rhythms adversely affects the well-being of the organism. This timekeeping system is generated and sustained by a genetically encoded endogenous mechanism composed of interlocking transcriptional/translational feedback loops that generate rhythmic expression of core clock genes. Genome-wide association studies (GWAS) and forward genetic studies show that SNPs in clock genes influence gene regulation and correlate with the risk of developing various conditions. We discuss genetic variations in core clock genes that are associated with various phenotypes, their implications for human health, and stress the need for thorough studies in this domain of circadian regulation.
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Affiliation(s)
- Jesse R Janoski
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Ignacio Aiello
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA
| | - Clayton W Lundberg
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Academy of Integrated Sciences, College of Science, Virginia Tech, Blacksburg, VA, USA
| | - Carla V Finkielstein
- Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA; Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA; Academy of Integrated Sciences, College of Science, Virginia Tech, Blacksburg, VA, USA.
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3
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Alwan IH, Aljubouri TRS, Al-Shuhaib MBS. A Novel Missense SNP in the Fatty Acid-Binding Protein 4 (FABP4) Gene is Associated with Growth Traits in Karakul and Awassi Sheep. Biochem Genet 2024; 62:1462-1484. [PMID: 37640973 DOI: 10.1007/s10528-023-10504-8] [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: 06/19/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
The fatty acid-binding protein 4 (FABP4) plays a crucial role in the transportation and metabolism of fatty acids. It binds to long-chain fatty acids and facilitates their transport within cells. FABP4 is involved in lipid metabolism, insulin sensitivity, inflammation, and energy homeostasis. This study was conducted to assess the association between the FABP4 gene and growth traits in Karakul and Awassi sheep. A PCR-single strand conformation polymorphism (SSCP) protocol was utilized to assess the polymorphism of FABP4 PCR products with growth traits measured at birth, three, six, nine, and twelve-month intervals. One non-synonymous SNP was identified in the second exon, in which threonine was converted to aspartate in the 61st position in FABP4 (p.61Thr > Asp). This novel SNP showed significant associations with all growth traits measured at all age intervals. The results showed that lambs with the TT genotype exhibited higher growth traits than those with the GT and GG genotypes, respectively. The conducted prediction showed a clearly deleterious effect of p.61Thr > Asp on FABP4 structure, which was accompanied by reduced fatty acid binding efficiency. Owing to the predicted damaging effects caused by p.61Thr > Asp on FABP, lower levels of lipid transport and its consequent increased weight gain and other growth trait indices are expected. Therefore, a putative mechanism through which lambs with these genotypes exhibit higher growth traits is proposed. The FABP4 gene is suggested as a promising marker to improve growth traits in Karakul and Awassi sheep. However, more research is required to validate this mechanism.
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Affiliation(s)
- Ibrahim H Alwan
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Thamer R S Aljubouri
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
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Kuznetsova KG, Vašíček J, Skiadopoulou D, Molnes J, Udler M, Johansson S, Njølstad PR, Manning A, Vaudel M. Bioinformatics pipeline for the systematic mining genomic and proteomic variation linked to rare diseases: The example of monogenic diabetes. PLoS One 2024; 19:e0300350. [PMID: 38635808 PMCID: PMC11025945 DOI: 10.1371/journal.pone.0300350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/23/2024] [Indexed: 04/20/2024] Open
Abstract
Monogenic diabetes is characterized as a group of diseases caused by rare variants in single genes. Like for other rare diseases, multiple genes have been linked to monogenic diabetes with different measures of pathogenicity, but the information on the genes and variants is not unified among different resources, making it challenging to process them informatically. We have developed an automated pipeline for collecting and harmonizing data on genetic variants linked to monogenic diabetes. Furthermore, we have translated variant genetic sequences into protein sequences accounting for all protein isoforms and their variants. This allows researchers to consolidate information on variant genes and proteins linked to monogenic diabetes and facilitates their study using proteomics or structural biology. Our open and flexible implementation using Jupyter notebooks enables tailoring and modifying the pipeline and its application to other rare diseases.
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Affiliation(s)
- Ksenia G. Kuznetsova
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jakub Vašíček
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Dafni Skiadopoulou
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Miriam Udler
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Pål Rasmus Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Alisa Manning
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States of America
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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5
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Aljubouri TRS, Al-Shuhaib MBS. A missense SNP in the proopiomelanocortin (POMC) gene is associated with growth traits in Awassi and Karakul sheep. Anim Biotechnol 2023; 34:4837-4850. [PMID: 37071507 DOI: 10.1080/10495398.2023.2197469] [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] [Indexed: 04/19/2023]
Abstract
This study was conducted to assess the association between proopiomelanocortin (POMC) gene and growth traits in Awassi and Karakul sheep. PCR-single strand conformation polymorphism (SSCP) method was utilized to assess the polymorphism of POMC PCR amplicons with body weight and length, wither and rump height, chest and abdominal circumference measured at birth, 3, 6, 9, and 12 months intervals. Only one missense SNP (rs424417456:C > A) was detected in exon-2, in which glycine was converted to cysteine in the 65th position in POMC (p.65Gly > Cys). rs424417456 SNP showed significant associations with all growth traits in the third, sixth, ninth, and twelfth months. At the age of 3 months onward, lambs with CC genotype showed higher body weight, body length, wither and rump heights, and chest and abdominal circumferences than lambs with CA and AA genotypes, respectively. Prediction analyses indicated a deleterious effect of p.65Gly > Cys on POMC structure, function, and stability. Owing to the strong correlation between rs424417456:CC and better growth characteristics, this genotype is proposed as a promising marker to enhance growth traits in Awassi and Karakul sheep. The predicted damaging effects caused by rs424417456:CA and rs424417456:AA genotypes may entail a putative mechanism through which lambs with these genotypes exhibit lower growth traits.
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Affiliation(s)
- Thamer R S Aljubouri
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Babil, Iraq
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Wigner-Jeziorska P, Grębowski R, Saluk J, Bijak M, Szemraj J. Polymorphic variations and mRNA expression of the genes encoding interleukins as well as enzymes of oxidative and nitrative stresses as a potential risk of nephrolithiasis development. PLoS One 2023; 18:e0293280. [PMID: 37878647 PMCID: PMC10599546 DOI: 10.1371/journal.pone.0293280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
Urolithiasis is one of the most common urological diseases worldwide with an unclear aetiology. However, a growing body of evidence suggests the potential role of molecular disturbances of the inflammation as well as oxidative and nitrative stresses, in the pathogenesis of urolithiasis. Therefore, we aimed to detect the potential association between six selected single-nucleotide polymorphisms (SNPs) and the development of nephrolithiasis. Moreover, we verified the association of urolithiasis development and mRNA expression of IL-6, IL-8, SOD2, and NOS2 in peripheral blood mononuclear cells (PBMCs). Total genomic DNA and mRNA were isolated from the peripheral blood of 112 patients with urolithiasis and 114 healthy subjects. Using Taq-Man® probes, we genotyped the following SNPs: rs1800797 and rs2069845 in IL-6, rs2227307 in IL-8, rs4880 in SOD2, rs2297518 and rs2779249 in NOS2. In turn, the evaluation of mRNA expression was performed using real-time PCR and 2-ΔCt methods. We found that the C/T genotype of the c.47 T>C-SOD2 SNP increased the frequency of urolithiasis occurrence whereas the T/T homozygote of the same polymorphism decreased the risk of urolithiasis development in the Polish population. Moreover, our study confirmed that patients with urolithiasis were characterised by decreased IL-6, IL-8, and SOD2 mRNA expression levels compared to the controls. In conclusion, our results suggest that polymorphic variants and changes in mRNA expression of IL-6, IL8, SOD2, and NOS2 may be involved in the pathophysiology of urolithiasis.
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Affiliation(s)
- Paulina Wigner-Jeziorska
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Radosław Grębowski
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
- Department of Urology, Provincial Integrated Hospital in Płock, Plock, Poland
| | - Joanna Saluk
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Michał Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
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7
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Galimova E, Rätsep R, Traks T, Chernov A, Gaysina D, Kingo K, Kõks S. Polymorphisms in corticotrophin-releasing hormone-proopiomalanocortin (CRH-POMC) system genes: Neuroimmune contributions to psoriasis disease. J Eur Acad Dermatol Venereol 2023; 37:2028-2040. [PMID: 37319102 DOI: 10.1111/jdv.19257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/03/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Skin is a target organ and source of the corticotropin-releasing hormone-proopiomelanocortin (CRH-POMC) system, operating as a coordinator and executor of responses to stress. Environmental stress exacerbates and triggers inflammatory skin diseases through modifying the cellular components of the immune system supporting the importance of CRH-POMC system in the pathogenesis of psoriasis. The aim of this study was to analyse the association of CRH-POMC polymorphisms with psoriasis and evaluate transcript expression of lesional psoriatic and normal skin in RNA-seq data. METHODS Samples of 104 patients with psoriasis and 174 healthy controls were genotyped for 42 single nucleotide polymorphisms (SNPs) of CRH-POMC using Applied Biosystems SNPlex™ method. The transcript quantification was performed using Salmon software v1.3.0. RESULTS This study demonstrated the associations between melanocortin 1 receptor (MC1R) polymorphisms rs2228479, rs3212369, dopachrome tautomerase (DCT) polymorphisms rs7987802, rs2031526, rs9524501 and psoriasis in the Tatar population. Very strong association was evident for the SNP rs7987802 in the DCT gene (pc = 5.95е-006) in psoriasis patients. Additionally, the haplotype analysis provided AT DCT (rs7992630 and rs7987802) and AGA MC1R (rs3212358, 2228479 and 885479) haplotypes significantly associated (pc ˂ 0.05) with psoriasis in the Tatar population, supporting the involvement of DCT and MC1R to the psoriasis susceptibility. Moreover, MC1R-203 and DCT-201 expression levels were decreased in psoriasis lesional skin compared with healthy control skin. CONCLUSIONS This study is the first to identify genetic variants of the MC1R and DCT genes significantly associated with psoriasis in Tatar population. Our results support potential roles of CRH-POMC system genes and DCT in the pathogenesis of psoriasis.
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Affiliation(s)
- Elvira Galimova
- Department of Physiology, University of Tartu, Tartu, Estonia
| | - Ranno Rätsep
- Department of Physiology, University of Tartu, Tartu, Estonia
| | - Tanel Traks
- Department of Dermatology and Venereology, University of Tartu, Tartu, Estonia
| | - Alexandr Chernov
- Department of Life Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Darya Gaysina
- School of Psychology, University of Sussex, Brighton, UK
| | - Külli Kingo
- Department of Dermatology and Venereology, University of Tartu, Tartu, Estonia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, University of Western Australia, Perth, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia, Australia
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8
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Ogiya D, Chyra Z, Verselis SJ, O'Keefe M, Cobb J, Abiatari I, Talluri S, Sithara AA, Hideshima T, Chu MP, Hájek R, Dorfman DM, Pilarski LM, Anderson KC, Adamia S. Identification of disease-related aberrantly spliced transcripts in myeloma and strategies to target these alterations by RNA-based therapeutics. Blood Cancer J 2023; 13:23. [PMID: 36737429 PMCID: PMC9898564 DOI: 10.1038/s41408-023-00791-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 12/17/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023] Open
Abstract
Novel drug discoveries have shifted the treatment paradigms of most hematological malignancies, including multiple myeloma (MM). However, this plasma cell malignancy remains incurable, and novel therapies are therefore urgently needed. Whole-genome transcriptome analyses in a large cohort of MM patients demonstrated that alterations in pre-mRNA splicing (AS) are frequent in MM. This manuscript describes approaches to identify disease-specific alterations in MM and proposes RNA-based therapeutic strategies to eradicate such alterations. As a "proof of concept", we examined the causes of aberrant HMMR (Hyaluronan-mediated motility receptor) splicing in MM. We identified clusters of single nucleotide variations (SNVs) in the HMMR transcript where the altered splicing took place. Using bioinformatics tools, we predicted SNVs and splicing factors that potentially contribute to aberrant HMMR splicing. Based on bioinformatic analyses and validation studies, we provided the rationale for RNA-based therapeutic strategies to selectively inhibit altered HMMR splicing in MM. Since splicing is a hallmark of many cancers, strategies described herein for target identification and the design of RNA-based therapeutics that inhibit gene splicing can be applied not only to other genes in MM but also more broadly to other hematological malignancies and solid tumors as well.
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Affiliation(s)
- Daisuke Ogiya
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Zuzana Chyra
- Department of Hemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic.,Department of Hemato-oncology, University of Ostrava, Ostrava, Czech Republic
| | - Sigitas J Verselis
- Molecular Diagnostic Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Morgan O'Keefe
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jacquelyn Cobb
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ivane Abiatari
- Institute of Medical and Public Health Research, School of Medicine, Ilia State University, Tbilisi, Georgia
| | - Srikanth Talluri
- Molecular Diagnostic Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA.,Veterans Administration Boston Healthcare System, West Roxbury, MA, USA
| | - Anjana Anilkumar Sithara
- Department of Hemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic.,Department of Hemato-oncology, University of Ostrava, Ostrava, Czech Republic
| | - Teru Hideshima
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Michael P Chu
- Department of Medicine, Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Roman Hájek
- Department of Hemato-oncology, University Hospital Ostrava, Ostrava, Czech Republic.,Department of Hemato-oncology, University of Ostrava, Ostrava, Czech Republic
| | - David M Dorfman
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Linda M Pilarski
- Department of Medicine, Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Sophia Adamia
- Jerome Lipper Multiple Myeloma Disease Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Institute of Medical and Public Health Research, School of Medicine, Ilia State University, Tbilisi, Georgia. .,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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9
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Wigner P, Dziedzic A, Synowiec E, Miller E, Bijak M, Saluk-Bijak J. Variation of genes encoding nitric oxide synthases and antioxidant enzymes as potential risks of multiple sclerosis development: a preliminary study. Sci Rep 2022; 12:10603. [PMID: 35732787 PMCID: PMC9217808 DOI: 10.1038/s41598-022-14795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
Multiple sclerosis (MS) is a neurodegenerative disease characterized by a variable clinical course and diverse pathophysiology, including nitrative and oxidative stresses as well as inflammation. We aimed to detect the potential association between five selected single-nucleotide polymorphisms (SNPs) in genes encoding nitric oxide synthetases as well as antioxidant enzymes and the development of MS in a Polish population. Genomic DNA was isolated from peripheral blood collected from 142 MS patients and 140 controls. Using Taq-Man® probes, we genotyped the following SNPs: rs1879417 in NOS1, and rs2297518 in NOS2 as well as rs4880 in SOD2, rs7943316 in CAT, rs713041 in GPX4. In the case of rs2297518, the C/C genotype and C allele SNP were associated with an enhanced occurrence of MS, while the C/T, T/T genotypes, and T allele of the same polymorphism reduced this risk. Moreover, the C/C homozygote and C allele of the rs4880 SNP reduced MS risk, while the T allele increased the risk. In addition, the A/T heterozygote of rs7943316 polymorphism was associated with an increased risk of MS occurrence. We also detected that the C/C genotype and C allele of rs713041 decreased the risk of MS, whereas the T/T genotype and T allele increased this risk. In conclusion, the results of our study suggest some links between polymorphic variability in the nitrative/oxidative stress-related genes and the risk of MS development in the Polish population.
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Affiliation(s)
- Paulina Wigner
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Angela Dziedzic
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
| | - Ewelina Synowiec
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska Street, 90-236, Lodz, Poland
| | - Elzbieta Miller
- Department of Neurological Rehabilitation, Medical University of Lodz, Milionowa 14, 93-113, Lodz, Poland
| | - Michal Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Joanna Saluk-Bijak
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
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10
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Single-Nucleotide Polymorphisms in Oxidative Stress-Related Genes and the Risk of a Stroke in a Polish Population-A Preliminary Study. Brain Sci 2021; 11:brainsci11030391. [PMID: 33808851 PMCID: PMC8003761 DOI: 10.3390/brainsci11030391] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/25/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
The present preliminary case-control study was undertaken to detect the potential association of six single nucleotide polymorphisms (SNPs) in oxidative stress-related genes: SOD2 (c.47T > C; rs4880), CAT (c.-89A > T; rs7943316), GPX4 (c.660T > A; rs713041), NOS1 (g.117803515C > T; rs1879417) and NOS2 (c.1823C > T; rs2297518 and c.-227G > C; rs10459953) and the occurrence of a stroke. The SNPs were determined using the TaqMan® Allelic Discrimination Assay in 107 patients with strokes and 107 age- and sex-matched individuals who had not experienced cerebrovascular accidents. The T alleles of the rs4880 were positively correlated with a stroke (bootstrap OR 1.31; 1.07-1.59 95% CI). In the case of the rs713041, an association with the T allele was found (bootstrap OR 1.36; 1.12-1.67). In addition, the occurrence of a stroke was associated with the presence of the C allele of the rs1879417 (bootstrap OR 1.32; 1.09-1.61). We also found that the C/C genotype and C allele of the rs2297518 increased the risk of a stroke (bootstrap ORs 7.00; 4.34-11.29 and 4.96; 3.88-6.34, respectively). Moreover, the C allele of the rs10459953 was associated with an increased occurrence of this disease (bootstrap OR 1.31; 1.08-1.60). These results indicated that genetics variants in the SOD2, GPX4, NOS1 and NOS2 might be associated with susceptibility to strokes in the Polish population.
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11
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Garrido-Martín D, Borsari B, Calvo M, Reverter F, Guigó R. Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. Nat Commun 2021; 12:727. [PMID: 33526779 PMCID: PMC7851174 DOI: 10.1038/s41467-020-20578-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it to analyze the GTEx dataset, generating a comprehensive catalog of sQTLs in the human genome. Downstream analysis of this catalog provides insight into the mechanisms underlying splicing regulation. We report that a core set of sQTLs is shared across multiple tissues. sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many also affect the expression of the same or other genes, uncovering regulatory loci that act through different mechanisms. sQTLs tend to be located in post-transcriptionally spliced introns, which would function as hotspots for splicing regulation. While many variants affect splicing patterns by altering the sequence of splice sites, many more modify the binding sites of RNA-binding proteins. Genetic variants affecting splicing can have a stronger phenotypic impact than those affecting gene expression.
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Affiliation(s)
- Diego Garrido-Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Catalonia, Spain.
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Catalonia, Spain
| | - Miquel Calvo
- Section of Statistics, Faculty of Biology, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona, 08028, Spain
| | - Ferran Reverter
- Section of Statistics, Faculty of Biology, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona, 08028, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Catalonia, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain.
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12
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Mucaki EJ, Shirley BC, Rogan PK. Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing. Front Genet 2020; 11:109. [PMID: 32211018 PMCID: PMC7066660 DOI: 10.3389/fgene.2020.00109] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
Splice isoform structure and abundance can be affected by either noncoding or masquerading coding variants that alter the structure or abundance of transcripts. When these variants are common in the population, these nonconstitutive transcripts are sufficiently frequent so as to resemble naturally occurring, alternative mRNA splicing. Prediction of the effects of such variants has been shown to be accurate using information theory-based methods. Single nucleotide polymorphisms (SNPs) predicted to significantly alter natural and/or cryptic splice site strength were shown to affect gene expression. Splicing changes for known SNP genotypes were confirmed in HapMap lymphoblastoid cell lines with gene expression microarrays and custom designed q-RT-PCR or TaqMan assays. The majority of these SNPs (15 of 22) as well as an independent set of 24 variants were then subjected to RNAseq analysis using the ValidSpliceMut web beacon (http://validsplicemut.cytognomix.com), which is based on data from the Cancer Genome Atlas and International Cancer Genome Consortium. SNPs from different genes analyzed with gene expression microarray and q-RT-PCR exhibited significant changes in affected splice site use. Thirteen SNPs directly affected exon inclusion and 10 altered cryptic site use. Homozygous SNP genotypes resulting in stronger splice sites exhibited higher levels of processed mRNA than alleles associated with weaker sites. Four SNPs exhibited variable expression among individuals with the same genotypes, masking statistically significant expression differences between alleles. Genome-wide information theory and expression analyses (RNAseq) in tumor exomes and genomes confirmed splicing effects for 7 of the HapMap SNP and 14 SNPs identified from tumor genomes. q-RT-PCR resolved rare splice isoforms with read abundance too low for statistical significance in ValidSpliceMut. Nevertheless, the web-beacon provides evidence of unanticipated splicing outcomes, for example, intron retention due to compromised recognition of constitutive splice sites. Thus, ValidSpliceMut and q-RT-PCR represent complementary resources for identification of allele-specific, alternative splicing.
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Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | | | - Peter K Rogan
- Department of Biochemistry, University of Western Ontario, London, ON, Canada.,CytoGnomix, London, ON, Canada.,Department of Oncology University of Western Ontario, London, ON, Canada.,Department of Computer Science, University of Western Ontario, London, ON, Canada
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13
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Malalla ZH, Al-Serri AE, AlAskar HM, Al-Kandari WY, Al-Bustan SA. Sequence analysis and variant identification at the APOC3 gene locus indicates association of rs5218 with BMI in a sample of Kuwaiti's. Lipids Health Dis 2019; 18:224. [PMID: 31856839 PMCID: PMC6921598 DOI: 10.1186/s12944-019-1165-6] [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: 09/16/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
Background APOC3 is important in lipid transport and metabolism with limited studies reporting genetic sequence variations in specific ethnic groups. The present study aimed to analyze the full APOC3 sequence among Kuwaiti Arabs and test the association of selected variants with lipid levels and BMI. Methods Variants were identified by Sanger sequencing the entire APOC3 gene in 100 Kuwaiti Arabs. Variants and their genotypes were fully characterized and used to construct haplotype blocks. Four variants (rs5128, rs2854117, rs2070668, KUAPOC3N3 g.5196 A > G) were selected for testing association with serum lipid levels and BMI in a cohort (n = 733). Results APOC3 sequence (4.3 kb) of a Kuwaiti Arab was deposited in Genbank (accession number KJ437193). Forty-two variants including 3 novels were identified including an “A” insertion at genomic positions 116,700,599–116,700,600 (promoter region) and two substitutions in intron 1 at genomic positions 116,700,819 and 116,701,159. Only three variants, (rs5128, rs2854117, and rs2070668) were analyzed for association of which rs5128 showed a trend for association with increased BMI, TG and VLDL levels that was further investigated using multivariate analysis. A significant association of rs5128 with BMI (p < 0.05) was observed following a dominant genetic model with increased risk by an OR of 4.022 (CI: 1.13–14.30). Conclusion The present study is the first to report sequence analysis of APOC3 in an Arab ethnic group. This study supports the inclusion of rs5128 as a marker for assessing genetic risk to dyslipidemia and obesity and the inclusion of the novel variant g.5196 A > G for population stratification of Arabs.
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Affiliation(s)
- Zainab H Malalla
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait, Kuwait
| | - Ahmad E Al-Serri
- Human Genetics Unit, Department of Pathology, Faculty of Medicine, Kuwait University, Hawally, Kuwait
| | - Huda M AlAskar
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait, Kuwait
| | - Wafaa Y Al-Kandari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait, Kuwait
| | - Suzanne A Al-Bustan
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait, Kuwait.
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14
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Vandiedonck C. Genetic association of molecular traits: A help to identify causative variants in complex diseases. Clin Genet 2019; 93:520-532. [PMID: 29194587 DOI: 10.1111/cge.13187] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022]
Abstract
In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies. The genetic variants that modulate them are called expression quantitative trait loci. Their study has been extended to other molecular quantitative trait loci (molQTLs) that regulate gene expression at the various levels, from chromatin state to cellular responses. Altogether, these studies have generated a wealth of basic information on the genome-wide patterns of gene expression and their inter-individual variation. Most importantly, molQTLs have become an invaluable asset in the genetic study of complex diseases. Although the identification of the disease-causing variants on the basis of their overlap with molQTLs requires caution, molQTLs can help to prioritize the relevant candidate gene(s) in the disease-associated regions and bring a functional interpretation of the associated variants, therefore, bridging the gap between genotypes and clinical phenotypes.
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Affiliation(s)
- C Vandiedonck
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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15
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Khazaal MS, Hamdan FB, Al-Mayah QS. Association of BCR/ABL transcript variants with different blood parameters and demographic features in Iraqi chronic myeloid leukemia patients. Mol Genet Genomic Med 2019; 7:e809. [PMID: 31206255 PMCID: PMC6687619 DOI: 10.1002/mgg3.809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 11/07/2022] Open
Abstract
Background Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm characterized by the presence of BCR‐ABL fusion gene (GenBank accession NC_000022.11). In the vast majority of CML patients, the typical subtype of BCR‐ABL transcript are b3a2, b2a2 or both. The aim of this study was to determine the different subtypes of BCR‐ABL transcript and their impact on the demographic and hematological parameters in Iraqi patients with CML. Methods One hundred patients with chronic phase CML (11 newly diagnosed and 89 imatinib‐resistant) were enrolled in this study. Ribonucleic acid (RNA) was extracted from leukocytes, and complementary DNA was created using reverse transcriptase polymerase chain reaction technique. A multiplex polymerase chain reaction with four specific primers was used to determine the BCR‐ABL fusion subtypes in each patient. Results Male to female ratio was 1.38:1. Fifty‐nine patients expressed b3a2 transcript, whereas 39 of the remaining cases were positive for b2a2 variant. One case expressed b2a3 transcript, while the last case coexpressed the two subtypes of mRNA b3a2/b2a2. Male and female were significantly associated with b3a2 and b2a2 subtypes, respectively. The b3a2 subtype showed higher total leukocyte count than b2a2 subgroup, while b2a2 variant demonstrated significantly elevated platelet counts compared to those with b3a2 transcript. A significantly higher plateletcrit percentage (PCT%) was found in patients with b2a2 transcript whereas. Conclusions The testified Iraqi group expressed M‐BCR‐ABL type with preponderance of b3a2 over b2a2 subtype. There was a gender‐skewed distribution in BCR‐ABL transcript types with b3a2 transcript more prevalent in males. The type of BCR‐ABL transcript is reflected by different leukocyte and platelet counts at diagnosis, which might represent a distinct phenotype and disease biology.
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Affiliation(s)
- Mahmood S Khazaal
- Department of Physiology, College of Medicine, Al-Nahrain University, Baghdad, Iraq
| | - Farqad B Hamdan
- Department of Physiology, College of Medicine, Al-Nahrain University, Baghdad, Iraq
| | - Qasim S Al-Mayah
- Medical Research Unit, College of Medicine, Al-Nahrain University, Baghdad, Iraq
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16
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The novel mutations in the MEF2C gene associate with growth of Nanjiang Yellow goats. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2018.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Haralambieva IH, Kennedy RB, Ovsyannikova IG, Schaid DJ, Poland GA. Current perspectives in assessing humoral immunity after measles vaccination. Expert Rev Vaccines 2019; 18:75-87. [PMID: 30585753 PMCID: PMC6413513 DOI: 10.1080/14760584.2019.1559063] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Repeated measles outbreaks in countries with relatively high vaccine coverage are mainly due to failure to vaccinate and importation; however, cases in immunized individuals exist raising questions about suboptimal measles vaccine-induced humoral immunity and/or waning immunity in a low measles-exposure environment. AREAS COVERED The plaque reduction neutralization measurement of functional measles-specific antibodies correlates with protection is the gold standard in measles serology, but it does not assess cellular-immune or other parameters that may be associated with durable and/or protective immunity after vaccination. Additional correlates of protection and long-term immunity and new determinants/signatures of vaccine responsiveness such as specific CD46 and IFI44L genetic variants associated with neutralizing antibody titers after measles vaccination are under investigation. Current and future systems biology studies, coupled with new technology/assays and analytical approaches, will lead to an increasingly sophisticated understanding of measles vaccine-induced humoral immunity and will identify 'signatures' of protective and durable immune responses. EXPERT OPINION This will translate into the development of highly predictive assays of measles vaccine efficacy, effectiveness, and durability for prospective identification of potential low/non-responders and susceptible individuals who require additional vaccine doses. Such new advances may drive insights into the development of new/improved vaccine formulations and delivery systems.
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Affiliation(s)
| | - Richard B Kennedy
- a Mayo Clinic Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
| | | | - Daniel J Schaid
- a Mayo Clinic Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
- b Department of Health Sciences Research , Mayo Clinic , Rochester , MN , USA
| | - Gregory A Poland
- a Mayo Clinic Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
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18
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Gui L, Jia J. Effect of single nucleotide polymorphisms in the UCP3 and FOXO1
genes on carcass quality traits in Qinchuan cattle. JOURNAL OF ANIMAL AND FEED SCIENCES 2018. [DOI: 10.22358/jafs/97366/2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Bahri BA, Daverdin G, Xu X, Cheng JF, Barry KW, Brummer EC, Devos KM. Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.). BMC Evol Biol 2018; 18:91. [PMID: 29898656 PMCID: PMC6000970 DOI: 10.1186/s12862-018-1193-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 05/15/2018] [Indexed: 11/24/2022] Open
Abstract
Background Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation. In this study, we analyzed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production to investigate signatures of selection that could have led to ecotype differentiation and to population adaptation to geographic zones. Results A total of 11,682 SNPs were mined from ~ 15 Gb of sequence data, out of which 251 SNPs were retained after filtering. Population structure analysis largely grouped upland accessions into one subpopulation and lowland accessions into two additional subpopulations. The most frequent SNPs were in homozygous state within accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to non-conservative amino acid changes. The non-conservative SNPs were largely in linkage disequilibrium with one haplotype being predominantly present in upland accessions while the other haplotype was commonly present in lowland accessions. Tajima’s test of neutrality indicated that PHYB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PHYB carried a SNP leading to a non-conservative amino acid change in the PAS domain, a region that acts as a sensor for light and oxygen in signal transduction. Conclusions Several non-conservative SNPs in genes potentially involved in plant architecture and adaptation have been identified and led to population structure and genetic differentiation of ecotypes in switchgrass. We suggest here that PHYB is a key gene involved in switchgrass natural selection. Further analyses are needed to determine whether any of the non-conservative SNPs identified play a role in the differential adaptation of upland and lowland switchgrass. Electronic supplementary material The online version of this article (10.1186/s12862-018-1193-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA. .,Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 43 Avenue Charles-Nicolle, 1082, Tunis, Tunisia.
| | - Guillaume Daverdin
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Present address: Vinson Edward Ltd, Faversham, ME13 8UP, UK
| | - Xiangyang Xu
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Present address: USDA-ARS, Wheat, Peanut and Other Field Crops Research Unit, Stillwater, OK, 74075, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, CA, 94598, USA
| | - Kerrie W Barry
- DOE Joint Genome Institute, Walnut Creek, California, CA, 94598, USA
| | - E Charles Brummer
- Plant Breeding Center, Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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20
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Lee CY, Lin HJ, Viswanath KK, Lin CP, Chang BCH, Chiu PH, Chiu CT, Wang RH, Chin SW, Chen FC. The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L. PLoS One 2018; 13:e0194605. [PMID: 29566053 PMCID: PMC5864051 DOI: 10.1371/journal.pone.0194605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/06/2018] [Indexed: 11/19/2022] Open
Abstract
Carica papaya L. is an important economic crop worldwide and is used as a model plant for sex-determination research. To study the different flower sex types, we screened sex-related genes using alternative splicing sequences (AS-seqs) from a transcriptome database of the three flower sex types, i.e., males, females, and hermaphrodites, established at 28 days before flowering using 15 bacterial artificial chromosomes (BACs) of C. papaya L. After screening, the cDNA regions of the three sex-related loci, including short vegetative phase-like (CpSVPL), the chromatin assembly factor 1 subunit A-like (CpCAF1AL), and the somatic embryogenesis receptor kinase (CpSERK), which contained eight sex-related single-nucleotide polymorphisms (SNPs) from the different sex types of C. papaya L., were genotyped using high-resolution melting (HRM). The three loci were examined regarding the profiles of the third whorl, as described below. CpSVPL, which had one SNP associated with the three sex genotypes, was highly expressed in the male and female sterile flowers (abnormal hermaphrodite flowers) that lacked the fourth whorl structure. CpCAF1AL, which had three SNPs associated with the male genotype, was highly expressed in male and normal hermaphrodite flowers, and had no AS-seqs, whereas it exhibited low expression and an AS-seqs in intron 11 in abnormal hermaphrodite flowers. Conversely, carpellate flowers (abnormal hermaphrodite flowers) showed low expression of CpSVPL and AS-seqs in introns 5, 6, and 7 of CpSERK, which contained four SNPs associated with the female genotype. Specifically, the CpSERK and CpCAF1AL loci exhibited no AS-seq expression in the third whorl of the male and normal hermaphrodite flowers, respectively, and variance in the AS-seq expression of all other types of flowers. Functional mapping of the third whorl of normal hermaphrodites indicated no AS-seq expression in CpSERK, low CpSVPL expression, and, for CpCAF1AL, high expression and no AS-seq expression on XYh-type chromosomes.
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Affiliation(s)
- Chen-Yu Lee
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
- * E-mail: (CYL); (FCC)
| | - Hui-Jun Lin
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kotapati Kasi Viswanath
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chih-Peng Lin
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | | | - Pei-Hsun Chiu
- Yourgene Bioscience, Shu-Lin District, New Taipei City, Taiwan
| | - Chan-Tai Chiu
- Pingtung Seed & Seedling Research Center, Taiwan Seed Improvement and Propagation Station, Pingtung, Taiwan
| | - Ren-Huang Wang
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, Pingtung, Taiwan
| | - Shih-Wen Chin
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Fure-Chyi Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
- * E-mail: (CYL); (FCC)
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21
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Tutakhel OAZ, Bianchi F, Smits DA, Bindels RJM, Hoenderop JGJ, van der Wijst J. Dominant functional role of the novel phosphorylation site S811 in the human renal NaCl cotransporter. FASEB J 2018; 32:4482-4493. [PMID: 29547703 DOI: 10.1096/fj.201701047r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The NaCl cotransporter (NCC) is essential for electrolyte homeostasis and control of blood pressure. The human SLC12A3 gene, which encodes NCC, gives rise to 3 isoforms, of which only the shortest isoform [NaCl cotransporter isoform 3 (NCC3)] has been studied extensively. All NCC isoforms share key phosphorylation sites at T55 and T60 that are essential mediators of NCC function. Recently, a novel phosphorylation site at S811 was identified in isoforms 1 and 2 [NaCl cotransporter splice variant (NCCSV)], which are only present in humans and higher primates. The aim of the current study, therefore, is to investigate the role of S811 phosphorylation in the regulation of NCC by a combination of biochemical and fluorescent microscopy analyses. We demonstrate that hypotonic low-chloride buffer increases S811 phosphorylation, whereas phosphorylation-deficient S811A mutant hinders phosphorylation at T55 and T60 in NCCSV and NCC3. NCCSV S811A impairs NCC3 activity in a dominant-negative fashion, although it does not affect plasma membrane abundance. This effect may be explained by the heterodimerization of NCCSV with NCC3. Taken together, our study highlights the dominant-negative effect of NCCSV on T55 and T60 phosphorylation and NCC activity. Here, we reveal a new function of NCCSV in humans that broadens the understanding on NCC regulation in blood pressure control.-Tutakhel, O. A. Z., Bianchi, F., Smits, D. A., Bindels, R. J. M., Hoenderop, J. G. J., van der Wijst, J. Dominant functional role of the novel phosphorylation site S811 in the human renal NaCl cotransporter.
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Affiliation(s)
- Omar A Z Tutakhel
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans Bianchi
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniël A Smits
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - René J M Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost G J Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jenny van der Wijst
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Lai MC, Bechy AL, Denk F, Collins E, Gavriliouk M, Zaugg JB, Ryan BJ, Wade-Martins R, Caffrey TM. Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders. Mol Neurodegener 2017; 12:79. [PMID: 29084565 PMCID: PMC5663040 DOI: 10.1186/s13024-017-0224-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome wide association studies have identified microtubule associated protein tau (MAPT) H1 haplotype single nucleotide polymorphisms (SNPs) as leading common risk variants for Parkinson's disease, progressive supranuclear palsy and corticobasal degeneration. The MAPT risk variants fall within a large 1.8 Mb region of high linkage disequilibrium, making it difficult to discern the functionally important risk variants. Here, we leverage the strong haplotype-specific expression of MAPT exon 3 to investigate the functionality of SNPs that fall within this H1 haplotype region of linkage disequilibrium. METHODS In this study, we dissect the molecular mechanisms by which haplotype-specific SNPs confer allele-specific effects on the alternative splicing of MAPT exon 3. Firstly, we use haplotype-hybrid whole-locus genomic MAPT vectors studies to identify functional SNPs. Next, we characterise the RNA-protein interactions at two loci by mass spectrometry. Lastly, we knockdown candidate splice factors to determine their effect on MAPT exon 3 using a novel allele-specific qPCR assay. RESULTS Using whole-locus genomic DNA expression vectors to express MAPT haplotype variants, we demonstrate that rs17651213 regulates exon 3 inclusion in a haplotype-specific manner. We further investigated the functionality of this region using RNA-electrophoretic mobility shift assays to show differential RNA-protein complex formation at the H1 and H2 sequence variants of SNP rs17651213 and rs1800547 and subsequently identified candidate trans-acting splicing factors interacting with these functional SNPs sequences by RNA-protein pull-down experiment and mass spectrometry. Finally, gene knockdown of candidate splice factors identified by mass spectrometry demonstrate a role for hnRNP F and hnRNP Q in the haplotype-specific regulation of exon 3 inclusion. CONCLUSIONS We identified common splice factors hnRNP F and hnRNP Q regulating the haplotype-specific splicing of MAPT exon 3 through intronic variants rs1800547 and rs17651213. This work demonstrates an integrated approach to characterise the functionality of risk variants in large regions of linkage disequilibrium.
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Affiliation(s)
- Mang Ching Lai
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anne-Laure Bechy
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Franziska Denk
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Emma Collins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Maria Gavriliouk
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Judith B. Zaugg
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Brent J. Ryan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX1 3QX UK
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX1 3QX UK
| | - Tara M. Caffrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
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Ranwez V, Serra A, Pot D, Chantret N. Domestication reduces alternative splicing expression variations in sorghum. PLoS One 2017; 12:e0183454. [PMID: 28886042 PMCID: PMC5590825 DOI: 10.1371/journal.pone.0183454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/06/2017] [Indexed: 01/09/2023] Open
Abstract
Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
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Affiliation(s)
| | - Audrey Serra
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
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Transcriptional signature of lymphoblastoid cell lines of BRCA1, BRCA2 and non- BRCA1/2 high risk breast cancer families. Oncotarget 2017; 8:78691-78712. [PMID: 29108258 PMCID: PMC5667991 DOI: 10.18632/oncotarget.20219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
Approximately 25% of hereditary breast cancer cases are associated with a strong familial history which can be explained by mutations in BRCA1 or BRCA2 and other lower penetrance genes. The remaining high-risk families could be classified as BRCAX (non-BRCA1/2) families. Gene expression involving alternative splicing represents a well-known mechanism regulating the expression of multiple transcripts, which could be involved in cancer development. Thus using RNA-seq methodology, the analysis of transcriptome was undertaken to potentially reveal transcripts implicated in breast cancer susceptibility and development. RNA was extracted from immortalized lymphoblastoid cell lines of 117 women (affected and unaffected) coming from BRCA1, BRCA2 and BRCAX families. Anova analysis revealed a total of 95 transcripts corresponding to 85 different genes differentially expressed (Bonferroni corrected p-value <0.01) between those groups. Hierarchical clustering allowed distinctive subgrouping of BRCA1/2 subgroups from BRCAX individuals. We found 67 transcripts, which could discriminate BRCAX from BRCA1/BRCA2 individuals while 28 transcripts discriminate affected from unaffected BRCAX individuals. To our knowledge, this represents the first study identifying transcripts differentially expressed in lymphoblastoid cell lines from major classes of mutation-related breast cancer subgroups, namely BRCA1, BRCA2 and BRCAX. Moreover, some transcripts could discriminate affected from unaffected BRCAX individuals, which could represent potential therapeutic targets for breast cancer treatment.
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25
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Genome-wide associations of CD46 and IFI44L genetic variants with neutralizing antibody response to measles vaccine. Hum Genet 2017; 136:421-435. [PMID: 28289848 DOI: 10.1007/s00439-017-1768-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/14/2017] [Indexed: 12/27/2022]
Abstract
Population-based studies have revealed 2-10% measles vaccine failure rate even after two vaccine doses. While the mechanisms behind this remain unknown, we hypothesized that host genetic factors are likely to be involved. We performed a genome-wide association study of measles specific neutralizing antibody and IFNγ ELISPOT response in a combined sample of 2872 subjects. We identified two distinct chromosome 1 regions (previously associated with MMR-related febrile seizures), associated with vaccine-induced measles neutralizing antibody titers. The 1q32 region contained 20 significant SNPs in/around the measles virus receptor-encoding CD46 gene, including the intronic rs2724384 (p value = 2.64 × 10-09) and rs2724374 (p value = 3.16 × 10-09) SNPs. The 1q31.1 region contained nine significant SNPs in/around IFI44L, including the intronic rs1333973 (p value = 1.41 × 10-10) and the missense rs273259 (His73Arg, p value = 2.87 × 10-10) SNPs. Analysis of differential exon usage with mRNA-Seq data and RT-PCR suggests the involvement of rs2724374 minor G allele in the CD46 STP region exon B skipping, resulting in shorter CD46 isoforms. Our study reveals common CD46 and IFI44L SNPs associated with measles-specific humoral immunity, and highlights the importance of alternative splicing/virus cellular receptor isoform usage as a mechanism explaining inter-individual variation in immune response after live measles vaccine.
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26
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Stein S, Bahrami-Samani E, Xing Y. Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants. Methods Mol Biol 2017; 1648:129-142. [PMID: 28766294 DOI: 10.1007/978-1-4939-7204-3_10] [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] [Indexed: 06/07/2023]
Abstract
RNA-seq is a powerful and popular technology for studying posttranscriptional regulation of gene expression, such as alternative splicing. The first step in analyzing RNA-seq data is to map the sequenced reads back to the genome. However, commonly used RNA-seq aligners use the consensus splice site dinucleotide motifs to map reads across splice junctions. This can be deceiving due to genomic variants that create novel splice site dinucleotides, leaving the personal splice junction reads un-mapped to the reference genome. We developed and evaluated a method called RNA Personal Genome Alignment Analyzer (rPGA) to identify "hidden" splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.
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Affiliation(s)
- Shayna Stein
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
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27
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Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Sci Rep 2016; 6:32406. [PMID: 27617755 PMCID: PMC5019111 DOI: 10.1038/srep32406] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/03/2016] [Indexed: 12/23/2022] Open
Abstract
Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.
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Affiliation(s)
- Pedro G. Ferreira
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Instituto de Investigação e Inovação em Saúde, (i3S) Universidade do Porto, 4200-625 Porto, Portugal
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-625 Porto, Portugal
| | - Martin Oti
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
| | - Matthias Barann
- Institute of Clinical Molecular Biology, Christians-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Suzana Ezquina
- Center for Human Genome and Stem-cell research (HUG-CELL), University of São Paulo (USP), 05508090 São Paulo, Brazil
| | - Marc R. Friedländer
- Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Manuel A. Rivas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Anna Esteve-Codina
- Centre Nacional d’Anàlisi Genòmica, 08028 Barcelona, Catalonia, Spain
- Center for Research in Agricultural Genomics (CRAG), Autonome University of Barcelona, 08193 Bellaterra, Catalonia, Spain
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christians-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Tuuli Lappalainen
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Pompeu Fabra University (UPF), 08003 Barcelona, Catalonia, Spain
| | - Michael Sammeth
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
- National Center of Scientific Computing (LNCC), 2233-6000 Petrópolis, Rio de Janeiro, Brazil
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28
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Nicot R, Vieira AR, Raoul G, Delmotte C, Duhamel A, Ferri J, Sciote JJ. ENPP1 and ESR1 genotypes influence temporomandibular disorders development and surgical treatment response in dentofacial deformities. J Craniomaxillofac Surg 2016; 44:1226-37. [PMID: 27519661 DOI: 10.1016/j.jcms.2016.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 06/04/2016] [Accepted: 07/13/2016] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Dentofacial deformities are dys-morpho-functional disorders involving the temporomandibular joints (TMJ). Many authors have reported a TMJ improvement in dysfunctional subjects with malocclusion after orthodontic or combined orthodontic and surgical treatment particularly for the relief of pain. In particular, few studies have highlighted the demographic and clinical predictors of response to surgical treatment. To date, no genetic factor has yet been identified as a predictor of response to surgical treatment. The aim of this cohort study is therefore to identify single-nucleotide polymorphisms associated with postoperative temporomandibular disorders (TMD) or with TMJ symptoms after orthognathic surgery. Here, we found the AA genotype of SNP rs1643821 (ESR1 gene) as a risk factor for dysfunctional worsening after orthognathic surgery. In addition, we have identified TT genotype of SNP rs858339 (ENPP1 gene) as a protective factor against TMD in a population of patients with dentofacial deformities. Conversely, the heterozygous genotype AT was identified as a risk factor of TMD with respect to the rest of our population. All these elements are particularly important to bring new screening strategies and tailor future treatment. PERSPECTIVE This study allows us to identify sub-populations at high risk of developing postoperative temporomandibular disorders after orthognathic surgery procedures. Many other genes of interest could be potential factors influencing the dysfunctional response to orthognathic surgery, particularly genes of the Opera cohort.
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Affiliation(s)
- Romain Nicot
- Univ. Lille, Oral and Maxillofacial Department, Roger Salengro Hospital, CHU Lille, F-59000, Lille, France.
| | - Alexandre R Vieira
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, 3501 Terrace St, Pittsburgh, PA 15261, USA.
| | - Gwénaël Raoul
- Univ. Lille, Oral and Maxillofacial Department, Roger Salengro Hospital, CHU Lille, INSERM U 1008, Controlled Drug Delivery Systems and Biomaterials, F-59000, Lille, France.
| | - Constance Delmotte
- Univ. Lille, Oral and Maxillofacial Department, Roger Salengro Hospital, CHU Lille, F-59000, Lille, France.
| | - Alain Duhamel
- Univ. Lille, CHU Lille, EA 2694 - Santé publique: épidémiologie et qualité des soins, F-59000, Lille, France.
| | - Joël Ferri
- Univ. Lille, Oral and Maxillofacial Department, Roger Salengro Hospital, CHU Lille, INSERM U 1008, Controlled Drug Delivery Systems and Biomaterials, F-59000, Lille, France.
| | - James J Sciote
- Department of Orthodontics, Kornberg School of Dentistry, Temple University, Philadelphia, PA 19140, USA.
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29
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Qu F, Qiao Q, Wang N, Ji G, Zhao H, He L, Wang H, Bao G. Genetic polymorphisms in circadian negative feedback regulation genes predict overall survival and response to chemotherapy in gastric cancer patients. Sci Rep 2016; 6:22424. [PMID: 26927666 PMCID: PMC4772484 DOI: 10.1038/srep22424] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/15/2016] [Indexed: 12/15/2022] Open
Abstract
Circadian negative feedback loop (CNFL) genes play important roles in cancer development and progression. To evaluate the effects of single nucleotide polymorphisms (SNPs) in CNFL genes on the survival of GC patients, 13 functional SNPs from 5 CNFL genes were genotyped in a cohort of 1030 resected GC patients (704 in the training set, 326 in the validation set) to explore the association of SNPs with overall survival (OS). Among the 13 SNPs, three SNPs (rs1056560 in CRY1, rs3027178 in PER1 and rs228729 in PER3) were significantly associated with OS of GC in the training set, and verified in the validation set and pooled analysis. Furthermore, a dose-dependent cumulative effect of these SNPs on GC survival was observed, and survival tree analysis showed higher order interactions between these SNPs. In addition, protective effect conferred by adjuvant chemotherapy (ACT) on GC was observed in patients with variant alleles (TG/GG) of rs1056560, but not in those with homozygous wild (TT) genotype. Functional assay suggested rs1056560 genotypes significantly affect CRY1 expression in cancer cells. Our study presents that SNPs in the CNFL genes may be associated with GC prognosis, and provides the guidance in selecting potential GC patients most likely responsive to ACT.
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Affiliation(s)
- Falin Qu
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an 710038, China.,93926 Army Hospital of PLA, Hetian 848000, China
| | - Qing Qiao
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an 710038, China
| | - Nan Wang
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an 710038, China
| | - Gang Ji
- Xijing Hospital of Digestive Disease, The Fourth Military Medical University, Xi'an, 710032 China
| | - Huadong Zhao
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an 710038, China
| | - Li He
- Department of Ophthalmology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Haichao Wang
- Department of Emergency Medicine, North Shore University Hospital, Manhasset, NY 11030, USA
| | - Guoqiang Bao
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an 710038, China
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30
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Nuvolone M, Hermann M, Sorce S, Russo G, Tiberi C, Schwarz P, Minikel E, Sanoudou D, Pelczar P, Aguzzi A. Strictly co-isogenic C57BL/6J-Prnp-/- mice: A rigorous resource for prion science. J Exp Med 2016; 213:313-27. [PMID: 26926995 PMCID: PMC4813672 DOI: 10.1084/jem.20151610] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/25/2016] [Indexed: 12/18/2022] Open
Abstract
Although its involvement in prion replication and neurotoxicity during transmissible spongiform encephalopathies is undisputed, the physiological role of the cellular prion protein (PrP(C)) remains enigmatic. A plethora of functions have been ascribed to PrP(C) based on phenotypes of Prnp(-/-) mice. However, all currently available Prnp(-/-) lines were generated in embryonic stem cells from the 129 strain of the laboratory mouse and mostly crossed to non-129 strains. Therefore, Prnp-linked loci polymorphic between 129 and the backcrossing strain resulted in systematic genetic confounders and led to erroneous conclusions. We used TALEN-mediated genome editing in fertilized mouse oocytes to create the Zurich-3 (ZH3) Prnp-ablated allele on a pure C57BL/6J genetic background. Genomic, transcriptional, and phenotypic characterization of Prnp(ZH3/ZH3) mice failed to identify phenotypes previously described in non-co-isogenic Prnp(-/-) mice. However, aged Prnp(ZH3/ZH3) mice developed a chronic demyelinating peripheral neuropathy, confirming the crucial involvement of PrP(C) in peripheral myelin maintenance. This new line represents a rigorous genetic resource for studying the role of PrP(C) in physiology and disease.
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Affiliation(s)
- Mario Nuvolone
- Institute of Neuropathology, University Hospital of Zurich, 8091 Zurich, Switzerland
| | - Mario Hermann
- Institute of Neuropathology, University Hospital of Zurich, 8091 Zurich, Switzerland Institute of Laboratory Animal Science, University of Zurich, 8091 Zurich, Switzerland
| | - Silvia Sorce
- Institute of Neuropathology, University Hospital of Zurich, 8091 Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Center Zurich (FGCZ), 8057 Zurich, Switzerland
| | - Cinzia Tiberi
- Institute of Neuropathology, University Hospital of Zurich, 8091 Zurich, Switzerland
| | - Petra Schwarz
- Institute of Neuropathology, University Hospital of Zurich, 8091 Zurich, Switzerland
| | - Eric Minikel
- Prion Alliance, Cambridge, MA 02139 Broad Institute, Cambridge, MA 02142 Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
| | - Despina Sanoudou
- Fourth Department of Internal Medicine, Attikon Hospital, Medical School, University of Athens, 115 27 Athens, Greece
| | - Pawel Pelczar
- Institute of Laboratory Animal Science, University of Zurich, 8091 Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital of Zurich, 8091 Zurich, Switzerland
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31
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Seibold P, Schmezer P, Behrens S, Michailidou K, Bolla MK, Wang Q, Flesch-Janys D, Nevanlinna H, Fagerholm R, Aittomäki K, Blomqvist C, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Lambrechts D, Wildiers H, Kristensen V, Alnæs GG, Nord S, Borresen-Dale AL, Hooning MJ, Hollestelle A, Jager A, Seynaeve C, Li J, Liu J, Humphreys K, Dunning AM, Rhenius V, Shah M, Kabisch M, Torres D, Ulmer HU, Hamann U, Schildkraut JM, Purrington KS, Couch FJ, Hall P, Pharoah P, Easton DF, Schmidt MK, Chang-Claude J, Popanda O. A polymorphism in the base excision repair gene PARP2 is associated with differential prognosis by chemotherapy among postmenopausal breast cancer patients. BMC Cancer 2015; 15:978. [PMID: 26674097 PMCID: PMC4682235 DOI: 10.1186/s12885-015-1957-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/27/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Personalized therapy considering clinical and genetic patient characteristics will further improve breast cancer survival. Two widely used treatments, chemotherapy and radiotherapy, can induce oxidative DNA damage and, if not repaired, cell death. Since base excision repair (BER) activity is specific for oxidative DNA damage, we hypothesized that germline genetic variation in this pathway will affect breast cancer-specific survival depending on treatment. METHODS We assessed in 1,408 postmenopausal breast cancer patients from the German MARIE study whether cancer specific survival after adjuvant chemotherapy, anthracycline chemotherapy, and radiotherapy is modulated by 127 Single Nucleotide Polymorphisms (SNPs) in 21 BER genes. For SNPs with interaction terms showing p<0.1 (likelihood ratio test) using multivariable Cox proportional hazard analyses, replication in 6,392 patients from nine studies of the Breast Cancer Association Consortium (BCAC) was performed. RESULTS rs878156 in PARP2 showed a differential effect by chemotherapy (p=0.093) and was replicated in BCAC studies (p=0.009; combined analysis p=0.002). Compared to non-carriers, carriers of the variant G allele (minor allele frequency=0.07) showed better survival after chemotherapy (combined allelic hazard ratio (HR)=0.75, 95% 0.53-1.07) and poorer survival when not treated with chemotherapy (HR=1.42, 95% 1.08-1.85). A similar effect modification by rs878156 was observed for anthracycline-based chemotherapy in both MARIE and BCAC, with improved survival in carriers (combined allelic HR=0.73, 95% CI 0.40-1.32). None of the SNPs showed significant differential effects by radiotherapy. CONCLUSIONS Our data suggest for the first time that a SNP in PARP2, rs878156, may together with other genetic variants modulate cancer specific survival in breast cancer patients depending on chemotherapy. These germline SNPs could contribute towards the design of predictive tests for breast cancer patients.
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Affiliation(s)
- Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69124, Heidelberg, Germany.
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Cancer Center Hamburg (UCCH), Hamburg, Germany.
- Department of Medical Biometrics and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Rainer Fagerholm
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Central Finland Health Care District, Jyväskylä Central Hospital, Jyväskylä, Finland.
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland.
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland.
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven, Belgium.
- Department of Oncology, Laboratory for Translational Genetics, University of Leuven, Leuven, Belgium.
| | - Hans Wildiers
- Department of General Medical Oncology, Multidisciplinary Breast Center, University Hospitals Leuven, Leuven, Belgium.
| | - Vessela Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
- Institute of Clinical Medicine, K.G. Jebsen Center for Breast Cancer Research, Faculty of Medicine, University of Oslo (UiO), Oslo, Norway.
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, University of Oslo (UiO), Oslo, Norway.
| | - Grethe Grenaker Alnæs
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
| | - Anne-Lise Borresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
- Institute of Clinical Medicine, K.G. Jebsen Center for Breast Cancer Research, Faculty of Medicine, University of Oslo (UiO), Oslo, Norway.
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Caroline Seynaeve
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore.
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore.
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Alison M Dunning
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Valerie Rhenius
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Mitul Shah
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia.
| | | | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA.
| | - Kristen S Purrington
- Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, Michigan, USA.
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Michigan, USA.
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Paul Pharoah
- Department of Oncology, Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Doug F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Odilia Popanda
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69124, Heidelberg, Germany.
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Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Res 2015; 43:10612-22. [PMID: 26578562 PMCID: PMC4678817 DOI: 10.1093/nar/gkv1099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/09/2015] [Indexed: 01/27/2023] Open
Abstract
RNA-seq has become a popular technology for studying genetic variation of pre-mRNA alternative splicing. Commonly used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across splice junctions. Consequently, genomic variants that create novel splice site dinucleotides may produce splice junction RNA-seq reads that cannot be mapped to the reference genome. We developed and evaluated an approach to identify ‘hidden’ splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Computational analysis and experimental validation indicate that this approach identifies personal specific splice junctions at a low false positive rate. Applying this approach to an RNA-seq data set of 75 individuals, we identified 506 personal specific splice junctions, among which 437 were novel splice junctions not documented in current human transcript annotations. 94 splice junctions had splice site SNPs associated with GWAS signals of human traits and diseases. These involve genes whose splicing variations have been implicated in diseases (such as OAS1), as well as novel associations between alternative splicing and diseases (such as ICA1). Collectively, our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.
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Affiliation(s)
- Shayna Stein
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhi-Xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. Brief Bioinform 2015; 17:841-62. [PMID: 26494363 DOI: 10.1093/bib/bbv084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Indexed: 12/20/2022] Open
Abstract
Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records.
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Association between the Advanced Glycosylation End Product-Specific Receptor Gene and Cardiovascular Death in Older Men. PLoS One 2015; 10:e0134475. [PMID: 26226616 PMCID: PMC4520603 DOI: 10.1371/journal.pone.0134475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/10/2015] [Indexed: 01/11/2023] Open
Abstract
Advanced glycosylation end product-specific receptor (AGER) signaling has been implicated in atherosclerosis. The aim of this study was to evaluate whether a common genetic variation in the AGER gene is associated with cardiovascular (CV) death. We included 1304 older men who were genotyped for rs1035798:C>T, which is a single nucleotide polymorphism (SNP) mapped to the third intron of AGER. Cox proportional hazard analysis was used to estimate the association of rs1035798:C>T with CV death. In addition we analyzed total RNA extracted from carotid atherosclerosis biopsies of 18 patients that did or did not have recent symptoms of cerebral embolization by quantitative real-time reverse transcription PCR (qRT-PCR). The minor T-allele of rs1035798:C>T was found to be associated with CV death under dominant (HR = 1.43, 95% CI: 1.01–2.02, P = 0.04) and recessive (HR = 2.05, 95% CI: 1.11–3.81, P = 0.02) models of inheritance even after adjustment for traditional cardiovascular risk factors. No association was found between rs1035798:C>T and non-CV death. qRT-PCR results suggested that median relative expression of AGER isoform 1 and isoform 6 transcripts were approximately 6- (P = 0.01) and 2-fold (P = 0.02) greater, respectively, within carotid biopsies of symptomatic compared to asymptomatic patients. These data suggest that the minor (T) allele of rs1035798:C>T represents an independent susceptibility factor for CV death. The expression of AGER isoforms is different in atheroma from patients with recent symptoms. Further studies are needed to investigate if rs1035798:C>T influences the alternative splicing of AGER.
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Characterization of a long-chain fatty acid-CoA ligase 1 gene and association between its SNPs and growth traits in the clam Meretrix meretrix. Gene 2015; 566:194-200. [PMID: 25900031 DOI: 10.1016/j.gene.2015.04.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/02/2015] [Accepted: 04/17/2015] [Indexed: 11/24/2022]
Abstract
Long-chain fatty acid-CoA ligases (ACSLs) play crucial roles in fatty acid (FA) metabolism. They convert free long-chain FA into acyl-CoAs, which are key intermediates in both anabolic and catabolic pathways. A long-chain fatty acid-CoA ligase gene was cloned in the clam Meretrix meretrix (MmeACSL1), with a full-length cDNA of 1865 bp encoding 475 amino acids. Its expression was only detected in hepatopancreas by semi-quantitative reverse transcription PCR. Expression level of MmeACSL1 exhibited a significant increase in a starvation experiment (P<0.05). This indicates that MmeACSL1 plays an important role in normal metabolism of M. meretrix and may be involved in energy supply and storage. Two exon SNPs and six intron SNPs were developed in this gene by direct sequencing. A marker-trait association analysis showed that five of these SNPs were significantly associated with growth traits (P<0.05). Also, haplotypes comprised of the five SNPs were revealed to be significantly growth-related (P<0.05), which further corroborates the relationship of this gene to growth traits of M. meretrix.
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Prayong P, Mairiang E, Pairojkul C, Chamgramol Y, Mairiang P, Bhudisawasdi V, Sripa B. An interleukin-6 receptor polymorphism is associated with opisthorchiasis-linked cholangiocarcinoma risk in Thailand. Asian Pac J Cancer Prev 2015; 15:5443-7. [PMID: 25041016 DOI: 10.7314/apjcp.2014.15.13.5443] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The cholangiocarcinoma (CCA) is a relatively rare cancer worldwide but it is highly prevalent in Thailand where the liver fluke, Opisthorchis viverrini is endemic. There are reports that interleukin 6 (IL-6) may play an important role in the pathogenesis of opisthorchiasis associated CCA. Functionally, IL-6 can act on target cells through its receptor, IL-6R, and IL-6R polymorphisms may affect the functional activity of IL-6 leading to susceptibility to cholangiocarcinogenesis. Therefore, we assessed the association of the 48892 A/C (Asp358Ala) polymorphism in exon 9 of the IL-6R gene in 79 CCA cases compared to 80 healthy controls using the PCR- RFLP technique. The results showed significant differences between CCA cases and controls in overall genotype (p=0.001) and allele frequencies (p=0.0002). Chi-square for trend test revealed a significant association between genotype and CCA susceptibility (p=0.0002). The odds ratios (ORs) for genotype were 0.283 (95% CI=0.131-0.605, AC vs. AA; p=0.0003) and 0.206 (95% CI=0.196-1.245, CC vs. AA; p=0.0416), the OR for alleles was 0.347 (95% CI=0.187-0.633, allele C vs. allele A; p=0.0002) and that for the carrier C variant was 0.272 (95% CI=0.130-0.564; p=0.0001). This study demonstrated a close association between an IL-6R polymorphism, specifically higher A allele, and cholangiocarcinoma.
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Affiliation(s)
- Pokpong Prayong
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand E-mail :
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Zhang Z, Wang X, Li R, Ju Z, Qi C, Zhang Y, Guo F, Luo G, Li Q, Wang C, Zhong J, Xu Y, Huang J. Genetic mutations potentially cause two novel NCF1 splice variants up-regulated in the mammary gland, blood and neutrophil of cows infected by Escherichia coli. Microbiol Res 2015; 174:24-32. [PMID: 25946326 DOI: 10.1016/j.micres.2015.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 11/18/2022]
Abstract
Neutrophil cytosolic factor 1 (NCF1) plays a crucial role in host defense against microbial pathogens. In this study, we investigated the potential alternative splicing patterns, expression and splice-relevant single nucleotide polymorphisms (SNPs) of the bovine NCF1 gene to increase insights into its potential role against bovine mastitis caused by Escherichia coli infection. Using RT-PCR and clone sequencing methods, we found two novel splice variants designed as NCF1-TV1 (retained intron 6) and NCF1-TV2 (retained part of intron 8), respectively, encoding two putative truncated proteins (239AA and 283AA). Two splice variants were drastically up-regulated in the mastitis-infected cows' mammary tissues, blood and neutrophils compared with these of healthy cows using real-time RT-PCR. Genomic sequencing analysis identified four novel SNPs g.10112 G>A, g.10766 T>C, SNPs g.12085 G>A and g.12430 T>C at the ends of intron 6 and intron 8 of NCF1. ESE motif predicted that the SNP (g.10766 T>C) might affect the binding with splicing-related factors and subsequently caused the production of aberrant splice variant NCF1-TV1, which is one of the potential reasons that the functional SNP was associated with increased milk somatic cell score in cow. Our results would help in better understanding the NCF1 gene function in the process against pathogen infection, and the effect of splicing-related SNP on the production of aberrant splice variant and careful functional characterization in dairy cattle.
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Affiliation(s)
- Zijing Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Rongling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Chao Qi
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Fang Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Guojing Luo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Qiuling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Yinxue Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1).
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Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV. Natural variation of gene models in Drosophila melanogaster. BMC Genomics 2015; 16:198. [PMID: 25888292 PMCID: PMC4373058 DOI: 10.1186/s12864-015-1415-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/28/2015] [Indexed: 09/03/2023] Open
Abstract
Background Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns. Results Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments. Conclusions Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1415-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yerbol Z Kurmangaliyev
- University of Southern California, Los Angeles, CA, USA. .,Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia.
| | - Alexander V Favorov
- Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Vavilov Institute of General Genetics, Moscow, Russia. .,Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia.
| | - Noha M Osman
- University of Southern California, Los Angeles, CA, USA. .,National Research Center, Dokki, Giza, Egypt.
| | - Kjong-Van Lehmann
- Memorial Sloan Kettering Cancer Center, Zuckerman Research Center, New York, NY, USA.
| | - Daniel Campo
- University of Southern California, Los Angeles, CA, USA.
| | | | - John Tower
- University of Southern California, Los Angeles, CA, USA.
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia. .,Lomonosov Moscow State University, Moscow, Russia.
| | - Sergey V Nuzhdin
- University of Southern California, Los Angeles, CA, USA. .,Saint Petersburg Polytechnical University, St Petersburg, Russia.
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Laurila K, Autio R, Kong L, Närvä E, Hussein S, Otonkoski T, Lahesmaa R, Lähdesmäki H. Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells. BioData Min 2014; 7:32. [PMID: 25649046 PMCID: PMC4298950 DOI: 10.1186/s13040-014-0032-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 12/04/2014] [Indexed: 11/13/2022] Open
Abstract
Background Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Several genome-wide studies have reported genomic variants that correlate with gene expression levels in various tissue and cell types. Results We studied human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) measuring the SNPs and CNVs with Affymetrix SNP 6 microarrays and expression values with Affymetrix Exon microarrays. We computed the linear relationships between SNPs and expression levels of exons, transcripts and genes, and the associations between gene CNVs and gene expression levels. Further, for a few of the resulted genes, the expression value was associated with both CNVs and SNPs. Our results revealed altogether 217 genes and 584 SNPs whose genomic alterations affect the transcriptome in the same cells. We analyzed the enriched pathways and gene ontologies within these groups of genes, and found out that the terms related to alternative splicing and development were enriched. Conclusions Our results revealed that in the human pluripotent stem cells, the expression values of several genes, transcripts and exons were affected due to the genomic variation. Electronic supplementary material The online version of this article (doi:10.1186/s13040-014-0032-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kirsti Laurila
- Department of Information and Computer Science, Aalto University School of Science, Espoo, Finland
| | - Reija Autio
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Lingjia Kong
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Elisa Närvä
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Samer Hussein
- Samuel Lunenfeld Research Institute, Toronto, Canada.,Research Program Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Research Program Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Harri Lähdesmäki
- Department of Information and Computer Science, Aalto University School of Science, Espoo, Finland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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40
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Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A. SNPlice: variants that modulate Intron retention from RNA-sequencing data. ACTA ACUST UNITED AC 2014; 31:1191-8. [PMID: 25481010 DOI: 10.1093/bioinformatics/btu804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 11/30/2014] [Indexed: 12/22/2022]
Abstract
RATIONALE The growing recognition of the importance of splicing, together with rapidly accumulating RNA-sequencing data, demand robust high-throughput approaches, which efficiently analyze experimentally derived whole-transcriptome splice profiles. RESULTS We have developed a computational approach, called SNPlice, for identifying cis-acting, splice-modulating variants from RNA-seq datasets. SNPlice mines RNA-seq datasets to find reads that span single-nucleotide variant (SNV) loci and nearby splice junctions, assessing the co-occurrence of variants and molecules that remain unspliced at nearby exon-intron boundaries. Hence, SNPlice highlights variants preferentially occurring on intron-containing molecules, possibly resulting from altered splicing. To illustrate co-occurrence of variant nucleotide and exon-intron boundary, allele-specific sequencing was used. SNPlice results are generally consistent with splice-prediction tools, but also indicate splice-modulating elements missed by other algorithms. SNPlice can be applied to identify variants that correlate with unexpected splicing events, and to measure the splice-modulating potential of canonical splice-site SNVs. AVAILABILITY AND IMPLEMENTATION SNPlice is freely available for download from https://code.google.com/p/snplice/ as a self-contained binary package for 64-bit Linux computers and as python source-code. CONTACT pmudvari@gwu.edu or horvatha@gwu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Prakriti Mudvari
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
| | - Mercedeh Movassagh
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
| | - Kamran Kowsari
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
| | - Ali Seyfi
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
| | - Maria Kokkinaki
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
| | - Nathan J Edwards
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
| | - Nady Golestaneh
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
| | - Anelia Horvath
- McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA McCormick Genomics and Proteomics Center, Department of Biochemistry and Molecular Medicine and Department of Pharmacology and Physiology, The George Washington University, Washington, DC 20037, USA and Department of Ophthalmology, Department of Neurology and Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, School of Medicine, Washington, DC 20057, USA
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Eight SNVs in NF-κB pathway genes and their different performances between subclinical mastitis and mixed Chinese Holstein cows. Gene 2014; 555:242-9. [PMID: 25447913 DOI: 10.1016/j.gene.2014.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 11/04/2014] [Accepted: 11/07/2014] [Indexed: 11/21/2022]
Abstract
The nuclear factor-kappa B (NF-κB) pathway proteins are key players in controlling both innate and adaptive immunity. However, the information on NF-κB pathway genes is very limited in mastitis resistance and milk production of Chinese Holstein cows. In this study, we examine the association of the NF-κB pathway gene variants with milk quality traits and somatic cell score (SCS) in Chinese Holstein cows. Eight single nucleotide variants (SNVs) were identified within the bovine NF-κB pathway genes, using DNA pooled sequencing, PCR-RFLP, and forced PCR-RFLP methods. These SNVs include SNV1: g. 536 C>T (exon 10 of Rel), SNV2: g. 94 G>A (exon 20 of p100), SNV3: g. 43 T>C (intron 6 of p105), SNV4: g. 2397 T>G (intron 9 of p105), SNV5: g. 382 G>C (intron 1 of IκBδ), SNV6: g. 21 C>T (exon 5 of IκBζ), SNV7: g. 272 G>A (intron 6 of IκBζ), and SNV8: g. 18 C>T (intron 10 of IκBζ). The association analysis in mixed Chinese Holstein population showed that SNV1 was significantly or highly significantly associated (P<0.01 and P<0.05) with fat rate, protein rate and SCS. Furthermore, the SNV1-CC (wild genotype) determined serine showed the significantly lower SCS and higher milk production traits compared to TT and TC. SNV2 was significantly associated (P<0.05) with SCS; SNV3 was significantly associated (P<0.05) with fat rate; and SNV4 was significantly associated (P<0.05) with fat rate and SCS. In 199 subclinical mastitis Chinese Holstein cows, the statistical results absolutely differed from the mixed Chinese Holstein individuals. Splice-site prediction by SplicePort showed that single nucleotide difference at eight SNVs results in the acceptor score and donor score changing obviously that may lead to alternative splicing. In brief, SNV1, SNV2, SNV3 and SNV4 could be useful genetic markers for mastitis resistance selection and breeding in Chinese Holstein cows. Furthermore, whether these SNVs lead to alternative splicing need further research.
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Zhang Z, Ma F, Zhou F, Chen Y, Wang X, Zhang H, Zhu Y, Bi J, Zhang Y. Functional polymorphisms of circadian negative feedback regulation genes are associated with clinical outcome in hepatocellular carcinoma patients receiving radical resection. Med Oncol 2014; 31:179. [PMID: 25344870 DOI: 10.1007/s12032-014-0179-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 08/10/2014] [Indexed: 01/27/2023]
Abstract
Previous studies have demonstrated that circadian negative feedback loop genes play an important role in the development and progression of many cancers. However, the associations between single-nucleotide polymorphisms (SNPs) in these genes and the clinical outcomes of hepatocellular carcinoma (HCC) after surgical resection have not been studied so far. Thirteen functional SNPs in circadian genes were genotyped using the Sequenom iPLEX genotyping system in a cohort of 489 Chinese HCC patients who received radical resection. Multivariate Cox proportional hazards model and Kaplan-Meier curve were used for the prognosis analysis. Cumulative effect analysis and survival tree analysis were used for the multiple SNPs analysis. Four individual SNPs, including rs3027178 in PER1, rs228669 and rs2640908 in PER3 and rs3809236 in CRY1, were significantly associated with overall survival (OS) of HCC patients, and three SNPs, including rs3027178 in PER1, rs228729 in PER3 and rs3809236 in CRY1, were significantly associated with recurrence-free survival (RFS). Moreover, we observed a cumulative effect of significant SNPs on OS and RFS (P for trend < 0.001 for both). Survival tree analysis indicated that wild genotype of rs228729 in PER3 was the primary risk factor contributing to HCC patients' RFS. Our study suggests that the polymorphisms in circadian negative feedback loop genes may serve as independent prognostic biomarkers in predicting clinical outcomes for HCC patients who received radical resection. Further studies with different ethnicities are needed to validate our findings and generalize its clinical utility.
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Affiliation(s)
- Zhaohui Zhang
- Department of Surgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, China
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Buas MF, Levine DM, Makar KW, Utsugi H, Onstad L, Li X, Galipeau PC, Shaheen NJ, Hardie LJ, Romero Y, Bernstein L, Gammon MD, Casson AG, Bird NC, Risch HA, Ye W, Liu G, Corley DA, Blount PL, Fitzgerald RC, Whiteman DC, Wu AH, Reid BJ, Vaughan TL. Integrative post-genome-wide association analysis of CDKN2A and TP53 SNPs and risk of esophageal adenocarcinoma. Carcinogenesis 2014; 35:2740-7. [PMID: 25280564 DOI: 10.1093/carcin/bgu207] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Incidence of esophageal adenocarcinoma (EA) in Western countries has increased markedly in recent decades. Although several risk factors have been identified for EA and its precursor, Barrett's esophagus (BE), including reflux, Caucasian race, male gender, obesity, and smoking, less is known about the role of inherited genetic variation. Frequent somatic mutations in the tumor suppressor genes CDKN2A and TP53 were recently reported in EA tumors, while somatic alterations at 9p (CDKN2A) and 17p (TP53) have been implicated as predictors of progression from BE to EA. Motivated by these findings, we used data from a genome-wide association study of 2515 EA cases and 3207 controls to analyze 37 germline single nucleotide polymorphisms at the CDKN2A and TP53 loci. Three CDKN2A polymorphisms were nominally associated (P < 0.05) with reduced risk of EA: rs2518720 C>T [intronic, odds ratio 0.90, P = 0.0121, q = 0.3059], rs3088440 G>A (3'UTR, odds ratio 0.84, P = 0.0186, q = 0.3059), and rs4074785 C>T (intronic, odds ratio 0.85, P = 0.0248, q = 0.3059). None of the TP53 single nucleotide polymorphisms reached nominal significance. Two of the CDKN2A variants identified were also associated with reduced risk of progression from BE to EA, when assessed in a prospective cohort of 408 BE patients: rs2518720 (hazard ratio 0.57, P = 0.0095, q = 0.0285) and rs3088440 (hazard ratio 0.34, P = 0.0368, q = 0.0552). In vitro functional studies of rs3088440, a single nucleotide polymorphism located in the seed sequence of a predicted miR-663b binding site, suggested a mechanism whereby the G>A substitution may attenuate miR-663b-mediated repression of the CDKN2A transcript. This study provides the first evidence that germline variation at the CDKN2A locus may influence EA susceptibility.
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Affiliation(s)
- Matthew F Buas
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98109, USA, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA,
| | - David M Levine
- Department of Biostatistics, University of Washington, School of Public Health, Seattle, WA 98109, USA
| | - Karen W Makar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Heidi Utsugi
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lynn Onstad
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaohong Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Patricia C Galipeau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicholas J Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Laura J Hardie
- Division of Epidemiology, University of Leeds, Leeds LS2 9JT, UK
| | - Yvonne Romero
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MI 55905, USA, The Romero Registry, Mayo Clinic, Rochester, MI 55905, USA
| | - Leslie Bernstein
- Department of Populations Sciences, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina School of Public Health, Chapel Hill, NC 27599, USA
| | - Alan G Casson
- Department of Surgery, University of Saskatchewan, Saskatoon S7N 5E5, Canada
| | - Nigel C Bird
- Department of Oncology, Medical School, University of Sheffield, Sheffield S10 2RX UK
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Geoffrey Liu
- Pharmacogenomic Epidemiology, Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94612 USA, San Francisco Medical Center, Kaiser Permanente Northern California, San Francisco, CA 94115 USA
| | - Patricia L Blount
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rebecca C Fitzgerald
- Medical Research Council (MRC) Cancer Cell Unit, Hutchison-MRC Research Centre and University of Cambridge, Cambridge CB2 0XZ UK
| | - David C Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane Queensland 4006, Australia and
| | - Anna H Wu
- Department of Preventive Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Brian J Reid
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Thomas L Vaughan
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, WA 98109, USA, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Liu J, Yu Y, Li F, Zhang X, Xiang J. A new anti-lipopolysaccharide factor (ALF) gene with its SNP polymorphisms related to WSSV-resistance of Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2014; 39:24-33. [PMID: 24769128 DOI: 10.1016/j.fsi.2014.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/10/2014] [Accepted: 04/14/2014] [Indexed: 06/03/2023]
Abstract
Anti-lipopolysaccharide factors (ALFs) of crustacean play an important role against bacteria or virus infection. In this study, the cDNA sequence and genomic sequence of one new isoform of ALF designated as nLvALF1 were reported. The open reading frame (ORF) of nLvALF1 consisted of 369 bp encoding 123 amino acids and the genomic structure of nLvALF1 comprised four introns and three exons. The predicted pI of the deduced protein was 8.82 and the molecular weight (MW) was 13.72 KDa. The deduced amino acid sequence of nLvALF1 contained a typical functional domain of ALF: LPS-binding domain. Phylogenetic analysis showed that nLvALF1 had the closest relationship with FcALF1 from Fenneropenaeus chinensis. The nLvALF1 was specifically expressed in lymphoid organ (Oka) of shrimp. Its transcriptional level was significantly up-regulated after white spot syndrome virus (WSSV) challenge, suggesting that nLvALF1 might participate in defense against WSSV in Litopenaeus vannamei. In order to search potential genetic markers associated with WSSV-resistance, we scanned the polymorphisms of the genomic fragment with 397 bp where the LPS-binding domain encoding sequence located and 18 SNPs were found. The distribution frequency of these SNPs was analyzed in WSSV susceptible shrimp and resistant shrimp separately. Significant differences existed in allelic frequencies at loci g.1361-T > C, g.1370-T > C, g.1419-T > A between the WSSV-resistant group and the WSSV-susceptible/susceptible group (P < 0.05). The specific haplotype CT consisted of g.1415-C > A and g.1419-T > A was associated with susceptibility to WSSV (P < 0.05). These findings provide theoretical support for selection of WSSV-resistant varieties of L. vannamei.
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Affiliation(s)
- Jingwen Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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Korir PK, Roberts L, Ramesar R, Seoighe C. A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing. BMC Res Notes 2014; 7:401. [PMID: 24969741 PMCID: PMC4084799 DOI: 10.1186/1756-0500-7-401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 06/13/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci - sQTLs). Genetic variants that affect mRNA splicing in trans are harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays. RESULTS Exon microarray data was generated from whole blood samples obtained from four individuals with a mutation in the splicing factor PRPF8 and four sibling controls. Although the mutation has no known phenotype in blood, there was evidence of widespread differences in splicing between cases and controls (affecting approximately 20% of exons). Most probesets with significantly different inclusion (defined as the expression intensity of the exon divided by the expression of the corresponding transcript) between cases and controls had higher inclusion in cases and corresponded to exons that were shorter than average, AT rich, located towards the 5' end of the gene and flanked by long introns. Introns flanking affected probesets were particularly depleted for the shortest category of introns, associated with splicing via intron definition. CONCLUSIONS Our results show that a mutation in a splicing factor, with a phenotype that is restricted to retinal tissue, acts as a trans-sQTL cluster in whole blood samples. Characteristics of the affected exons suggest that they are spliced co-transcriptionally and via exon definition. However, due to the small sample size available for this study, further studies are required to confirm the widespread impact of this PRPF8 mutation on mRNA splicing outside the retina.
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Affiliation(s)
- Paul K Korir
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, University Road, Galway, Republic of Ireland
| | - Lisa Roberts
- UCT/MRC Human Genetics Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Raj Ramesar
- UCT/MRC Human Genetics Research Unit, Division of Human Genetics, Institute for Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, University Road, Galway, Republic of Ireland
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Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation. QUANTITATIVE BIOLOGY 2014. [DOI: 10.1007/s40484-014-0031-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Jung H, Lyons RE, Li Y, Thanh NM, Dinh H, Hurwood DA, Salin KR, Mather PB. A candidate gene association study for growth performance in an improved giant freshwater prawn (Macrobrachium rosenbergii ) culture line. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:161-180. [PMID: 24122143 DOI: 10.1007/s10126-013-9555-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 08/06/2013] [Indexed: 06/02/2023]
Abstract
A candidate gene approach using type I single nucleotide polymorphism (SNP) markers can provide an effective method for detecting genes and gene regions that underlie phenotypic variation in adaptively significant traits. In the absence of available genomic data resources, transcriptomes were recently generated in Macrobrachium rosenbergii to identify candidate genes and markers potentially associated with growth. The characterisation of 47 candidate loci by ABI re-sequencing of four cultured and eight wild samples revealed 342 putative SNPs. Among these, 28 SNPs were selected in 23 growth-related candidate genes to genotype in 200 animals selected for improved growth performance in an experimental GFP culture line in Vietnam. The associations between SNP markers and individual growth performance were then examined. For additive and dominant effects, a total of three exonic SNPs in glycogen phosphorylase (additive), heat shock protein 90 (additive and dominant) and peroxidasin (additive), and a total of six intronic SNPs in ankyrin repeats-like protein (additive and dominant), rolling pebbles (dominant), transforming growth factor-β induced precursor (dominant), and UTP-glucose-1-phosphate uridylyltransferase 2 (dominant) genes showed significant associations with the estimated breeding values in the experimental animals (P =0.001-0.031). Individually, they explained 2.6-4.8 % of the genetic variance (R²=0.026-0.048). This is the first large set of SNP markers reported for M. rosenbergii and will be useful for confirmation of associations in other samples or culture lines as well as having applications in marker-assisted selection in future breeding programs.
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Li JW, Lai KP, Ching AKK, Chan TF. Transcriptome sequencing of Chinese and Caucasian population identifies ethnic-associated differential transcript abundance of heterogeneous nuclear ribonucleoprotein K (hnRNPK). Genomics 2013; 103:56-64. [PMID: 24373910 DOI: 10.1016/j.ygeno.2013.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/06/2013] [Accepted: 12/18/2013] [Indexed: 01/22/2023]
Abstract
Gene expression variations (GEV) among different ethnic groups have been a subject matter for extensive study. Relatively less known is the extent of alternative splicing variations (ASV) in the context of ethnicity. We conducted a transcriptome sequencing study of 20 lymphoblastoid cell lines obtained from Caucasian and Han Chinese, and identified known genes that exhibit differential isoform abundance between the two ethnic groups. Among them hnRNPK, a co-factor of p53 (TP53), could be further replicated in a 39-sample cohort with TaqMan assay. Although within-population novel splice variants are common, inter-population novel splice variants are rare. We further analyzed 5.63 billion sequencing reads retrieved from the NCBI Sequence Read Archive and identified potential ethnic-specific transcribed regions.
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Affiliation(s)
- Jing-Woei Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Keng-Po Lai
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Arthur K K Ching
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Slominski AT, Zmijewski MA, Zbytek B, Tobin DJ, Theoharides TC, Rivier J. Key role of CRF in the skin stress response system. Endocr Rev 2013; 34:827-84. [PMID: 23939821 PMCID: PMC3857130 DOI: 10.1210/er.2012-1092] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 08/02/2013] [Indexed: 02/08/2023]
Abstract
The discovery of corticotropin-releasing factor (CRF) or CRH defining the upper regulatory arm of the hypothalamic-pituitary-adrenal (HPA) axis, along with the identification of the corresponding receptors (CRFRs 1 and 2), represents a milestone in our understanding of central mechanisms regulating body and local homeostasis. We focused on the CRF-led signaling systems in the skin and offer a model for regulation of peripheral homeostasis based on the interaction of CRF and the structurally related urocortins with corresponding receptors and the resulting direct or indirect phenotypic effects that include regulation of epidermal barrier function, skin immune, pigmentary, adnexal, and dermal functions necessary to maintain local and systemic homeostasis. The regulatory modes of action include the classical CRF-led cutaneous equivalent of the central HPA axis, the expression and function of CRF and related peptides, and the stimulation of pro-opiomelanocortin peptides or cytokines. The key regulatory role is assigned to the CRFR-1α receptor, with other isoforms having modulatory effects. CRF can be released from sensory nerves and immune cells in response to emotional and environmental stressors. The expression sequence of peptides includes urocortin/CRF→pro-opiomelanocortin→ACTH, MSH, and β-endorphin. Expression of these peptides and of CRFR-1α is environmentally regulated, and their dysfunction can lead to skin and systemic diseases. Environmentally stressed skin can activate both the central and local HPA axis through either sensory nerves or humoral factors to turn on homeostatic responses counteracting cutaneous and systemic environmental damage. CRF and CRFR-1 may constitute novel targets through the use of specific agonists or antagonists, especially for therapy of skin diseases that worsen with stress, such as atopic dermatitis and psoriasis.
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Affiliation(s)
- Andrzej T Slominski
- MD, PhD, Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center; 930 Madison Avenue, Suite 500, Memphis, Tennessee 38163.
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Wang J, Nong L, Wei Y, Qin S, Zhou Y, Tang Y. Association of osteopontin polymorphisms with nasopharyngeal carcinoma risk. Hum Immunol 2013; 75:76-80. [PMID: 24120738 DOI: 10.1016/j.humimm.2013.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 09/05/2013] [Accepted: 09/27/2013] [Indexed: 12/12/2022]
Abstract
No previous study has reported the association of osteopontin polymorphisms with nasopharyngeal carcinoma (NPC) risk. We aimed to investigate the association in a Chinese population. Four variants of osteopontin, rs11730582, rs1126772, rs9138, and rs4754 polymorphisms, were assessed in a case-control study which consists of 108 NPC patients and 210 health controls, by using polymerase chain reaction--restriction fragment length polymorphism method. Serum osteopontin levels were measured by enzyme-linked immunosorbent assay. The serum osteopontin levels were significantly higher in NPC patients than those in controls (P<0.01). Carriers of CC and CT genotype of rs11730582 presented lower serum osteopontin levels than those of TT genotype carriers (P<0.05). Genotypes CT and CT+CC of rs11730582 were associated with the risk of NPC (CT:OR = 0.57, 95%CI = 0.34-0.94; CC+CT:OR = 0.54, 95%CI = 0.34-0.87). Haplotype analysis revealed that haplotype T-A-A-C of rs11730582, rs1126772, rs9138, and rs4754 was associated with NPC risk (OR = 0.49, 95%CI = 0.27-0.86). Stratification analysis showed that genotypes CT and CT+CC of rs11730582 were associated with tumor stage and lymph node metastasis (P<0.05). No associations were found between rs1126772, rs9138, and rs4754 polymorphisms and NPC risk (P>0.05). The variant rs11730582 of osteopontin is associated with NPC risk. It potentially serves as a genetic marker of NPC predisposition.
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Affiliation(s)
- Junli Wang
- Center of Clinical Laboratory, Affiliated Hospital of Youjiang Medical College for Nationalities, Baise 533000, Guangxi, China
| | - Legen Nong
- Center of Clinical Laboratory, Affiliated Hospital of Youjiang Medical College for Nationalities, Baise 533000, Guangxi, China
| | - Yesheng Wei
- Center of Clinical Laboratory, Affiliated Hospital of Youjiang Medical College for Nationalities, Baise 533000, Guangxi, China
| | - Shanyu Qin
- First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - You Zhou
- Minerva Foundation Institute for Medical Research, FI-00290 Helsinki, Finland.
| | - Yujin Tang
- Affiliated Hospital of Youjiang Medical College for Nationalities, Baise 533000, Guangxi, China.
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