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Chappell K, Ait Tayeb AEK, Colle R, Bouligand J, El-Asmar K, Gressier F, Trabado S, David DJ, Feve B, Becquemont L, Corruble E, Verstuyft C. The association of ARRB1 polymorphisms with response to antidepressant treatment in depressed patients. Front Pharmacol 2022; 13:974570. [PMID: 36386175 PMCID: PMC9644891 DOI: 10.3389/fphar.2022.974570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/11/2022] [Indexed: 09/02/2023] Open
Abstract
Introduction: β-arrestin 1, a protein encoded by ARRB1 involved in receptor signaling, is a potential biomarker for the response to antidepressant drug (ATD) treatment in depression. We examined ARRB1 genetic variants for their association with response following ATD treatment in METADAP, a cohort of 6-month ATD-treated depressed patients. Methods: Patients (n = 388) were assessed at baseline (M0) and after 1 (M1), 3 (M3), and 6 months (M6) of treatment for Hamilton Depression Rating Scale (HDRS) changes, response, and remission. Whole-gene ARRB1 variants identified from high-throughput sequencing were separated by a minor allele frequency (MAF)≥5%. Frequent variants (i.e., MAF≥5%) annotated by RegulomeDB as likely affecting transcription factor binding were analyzed using mixed-effects models. Rare variants (i.e., MAF<5%) were analyzed using a variant set analysis. Results: The variant set analysis of rare variants was significant in explaining HDRS score changes (T = 878.9; p = 0.0033) and remission (T = -1974.1; p = 0.034). Rare variant counts were significant in explaining response (p = 0.016), remission (p = 0.022), and HDRS scores at M1 (p = 0.0021) and M3 (p=<0.001). rs553664 and rs536852 were significantly associated with the HDRS score (rs553664: p = 0.0055 | rs536852: p = 0.046) and remission (rs553664: p = 0.026 | rs536852: p = 0.012) through their interactions with time. At M6, significantly higher HDRS scores were observed in rs553664 AA homozygotes (13.98 ± 1.06) compared to AG heterozygotes (10.59 ± 0.86; p = 0.014) and in rs536852 GG homozygotes (14.88 ± 1.10) compared to AG heterozygotes (11.26 ± 0.95; p = 0.0061). Significantly lower remitter rates were observed in rs536852 GG homozygotes (8%, n = 56) compared to AG heterozygotes (42%, n = 105) at M6 (p = 0.0018). Conclusion: Our results suggest ARRB1 variants may influence the response to ATD treatment in depressed patients. Further analysis of functional ARRB1 variants and rare variant burden in other populations would help corroborate our exploratory analysis. β-arrestin 1 and genetic variants of ARRB1 may be useful clinical biomarkers for clinical improvement following ATD treatment in depressed individuals. Clinical Trial Registration: clinicaltrials.gov; identifier NCT00526383.
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Affiliation(s)
- Kenneth Chappell
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
| | - Abd El Kader Ait Tayeb
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
- Service Hospitalo-Universitaire de Psychiatrie de Bicêtre, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Romain Colle
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
- Service Hospitalo-Universitaire de Psychiatrie de Bicêtre, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Jérôme Bouligand
- INSERM UMR-S U1185, Faculté de Médecine, University Paris-Saclay, Le Kremlin Bicêtre, France
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Khalil El-Asmar
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
- Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Florence Gressier
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
- Service Hospitalo-Universitaire de Psychiatrie de Bicêtre, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Séverine Trabado
- INSERM UMR-S U1185, Faculté de Médecine, University Paris-Saclay, Le Kremlin Bicêtre, France
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Denis Joseph David
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
- CESP, MOODS Team, INSERM UMR 1018, Faculté de Médecine, University Paris-Saclay, Le Kremlin Bicêtre, France
| | - Bruno Feve
- Sorbonne Université-INSERM, Centre de Recherche Saint-Antoine, UMR S938, Institut Hospitalo-Universitaire ICAN, Service d’Endocrinologie, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Centre de Référence des Maladies Rares de l’Insulino-Sécrétion et de l’Insulino-Sensibilité, Paris, France
| | - Laurent Becquemont
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
- Centre de Recherche Clinique Paris-Saclay, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
| | - Emmanuelle Corruble
- Service Hospitalo-Universitaire de Psychiatrie de Bicêtre, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
- CESP, MOODS Team, INSERM UMR 1018, Faculté de Médecine, University Paris-Saclay, Le Kremlin Bicêtre, France
| | - Céline Verstuyft
- Université Paris-Saclay, UMR 1018, CESP-Inserm, Team MOODS, Faculté de Pharmacie, Bâtiment Henri MOISSAN, Orsay, France
- Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
- Centre de Ressources Biologiques Paris-Saclay, Hôpitaux Universitaires Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Le Kremlin Bicêtre, France
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Favia M, Fitak R, Guerra L, Pierri CL, Faye B, Oulmouden A, Burger PA, Ciani E. Beyond the Big Five: Investigating Myostatin Structure, Polymorphism and Expression in Camelus dromedarius. Front Genet 2019; 10:502. [PMID: 31231423 PMCID: PMC6566074 DOI: 10.3389/fgene.2019.00502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/07/2019] [Indexed: 12/19/2022] Open
Abstract
Myostatin, a negative regulator of skeletal muscle mass in animals, has been shown to play a role in determining muscular hypertrophy in several livestock species, and a high degree of polymorphism has been previously reported for this gene in humans and cattle. In this study, we provide a characterization of the myostatin gene in the dromedary (Camelus dromedarius) at the genomic, transcript and protein level. The gene was found to share high structural and sequence similarity with other mammals, notably Old World camelids. 3D modeling highlighted several non-conservative SNP variants compared to the bovine, as well as putative functional variants involved in the stability of the myostatin dimer. NGS data for nine dromedaries from various countries revealed 66 novel SNPs, all of them falling either upstream or downstream the coding region. The analysis also confirmed the presence of three previously described SNPs in intron 1, predicted here to alter both splicing and transcription factor binding sites (TFBS), thus possibly impacting myostatin processing and/or regulation. Several putative TFBS were identified in the myostatin upstream region, some of them belonging to the myogenic regulatory factor family. Patterns of SNP distribution across countries, as suggested by Bayesian clustering of the nine dromedaries using the 69 SNPs, pointed to weak geographic differentiation, in line with known recurrent gene flow at ancient trading centers along caravan routes. Myostatin expression was investigated in a set of 8 skeletal muscles, both at transcript and protein level, via Digital Droplet PCR and Western Blotting, respectively. No significant differences were observed at the transcript level, while, at the protein level, the only significant differences concerned the promyostatin dimer (75 kDa), in four pair-wise comparisons, all involving the tensor fasciae latae muscle. Beside the mentioned band at 75 kDa, additional bands were observed at around 40 and 25 kDa, corresponding to the promyostatin monomer and the active C-terminal myostatin dimer, respectively. Their weaker intensity suggests that the unprocessed myostatin dimers could act as important reservoirs of slowly available myostatin forms. Under this assumption, the sequential cleavage steps may contribute additional layers of control within an already complex regulatory framework.
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Affiliation(s)
- Maria Favia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Robert Fitak
- Research Institute of Wildlife Ecology, Vetmeduni, Vienna, Austria.,Department of Biology, Duke University, Durham, NC, United States
| | - Lorenzo Guerra
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | | | - Ahmad Oulmouden
- Département Sciences du Vivant, Université de Limoges, Limoges, France
| | | | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
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Miller JE, Veturi Y, Ritchie MD. Innovative strategies for annotating the "relationSNP" between variants and molecular phenotypes. BioData Min 2019; 12:10. [PMID: 31114635 PMCID: PMC6518798 DOI: 10.1186/s13040-019-0197-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 11/10/2022] Open
Abstract
Characterizing how variation at the level of individual nucleotides contributes to traits and diseases has been an area of growing interest since the completion of sequencing the first human genome. Our understanding of how a single nucleotide polymorphism (SNP) leads to a pathogenic phenotype on a genome-wide scale is a fruitful endeavor for anyone interested in developing diagnostic tests, therapeutics, or simply wanting to understand the etiology of a disease or trait. To this end, many datasets and algorithms have been developed as resources/tools to annotate SNPs. One of the most common practices is to annotate coding SNPs that affect the protein sequence. Synonymous variants are often grouped as one type of variant, however there are in fact many tools available to dissect their effects on gene expression. More recently, large consortiums like ENCODE and GTEx have made it possible to annotate non-coding regions. Although annotating variants is a common technique among human geneticists, the constant advances in tools and biology surrounding SNPs requires an updated summary of what is known and the trajectory of the field. This review will discuss the history behind SNP annotation, commonly used tools, and newer strategies for SNP annotation. Additionally, we will comment on the caveats that distinguish approaches from one another, along with gaps in the current state of knowledge, and potential future directions. We do not intend for this to be a comprehensive review for any specific area of SNP annotation, but rather it will be an excellent resource for those unfamiliar with computational tools used to functionally characterize SNPs. In summary, this review will help illustrate how each SNP annotation method impacts the way in which the genetic and molecular etiology of a disease is explored in-silico.
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Affiliation(s)
- Jason E. Miller
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Yogasudha Veturi
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Marylyn D. Ritchie
- Department of Genetics, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
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D'Aquila P, Crocco P, De Rango F, Indiveri C, Bellizzi D, Rose G, Passarino G. A Genetic Variant of ASCT2 Hampers In Vitro RNA Splicing and Correlates with Human Longevity. Rejuvenation Res 2018; 21:193-199. [DOI: 10.1089/rej.2017.1948] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Patrizia D'Aquila
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Francesco De Rango
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Cesare Indiveri
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Giuseppina Rose
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Science, University of Calabria, Rende, Italy
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Zhu Y, Guo L, Wang S, Yu Q, Lu J. Association of Smoking and XPG, CYP1A1, OGG1, ERCC5, ERCC1, MMP2, and MMP9 Gene Polymorphisms with the early detection and occurrence of Laryngeal Squamous Carcinoma. J Cancer 2018; 9:968-977. [PMID: 29581776 PMCID: PMC5868164 DOI: 10.7150/jca.22841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 01/16/2018] [Indexed: 11/05/2022] Open
Abstract
A total of 200 smoking-related laryngeal carcinoma patients with pathology confirmation from the Eye and ENT Hospital and 190 high-risk smokers were included in a survey. All of the participants had a smoking index greater than 400 (cigarettes/day*year.) We obtained data on clinical and baseline characteristics, and peripheral blood was obtained and subjected to DNA extraction to analyse the correlation between smoking and the occurrence of laryngeal carcinoma. We selected candidate genes and SNP fragments that were found to be closely associated with smoking-related tumours in preliminary studies. The selected candidate genes were XPG, CYP1A1, OGG1, ERCC5, ERCC1, MMP2, and MMP9. We then performed SNP sequencing using Sequenom SNP detection technology. Target genes and single nucleotide polymorphism (SNP) fragments were evaluated to analyse the correlation between genotype or allele and smoking-related laryngeal carcinoma and to identify susceptibility genes related to laryngeal carcinoma. The results included four main findings: (1) The smoking index differed significantly between laryngeal cancer patients and control subjects (P=0.0035). The risk of laryngeal cancer was increased among individuals with a smoking index greater than 600 cigarettes/day*year (P=0.03). (2) The smoking index was significantly correlated with the T, N and clinical stages (P<0.05). (3) The polymorphisms CYP1A1-rs1048943, rs4646421, and rs4646422 and MMP9-rs17577 were significantly associated with laryngeal squamous carcinoma (P<0.05). (4) After stratifying the subjects by smoking degree, the GT genotype of ERCC1-rs2298881 was associated with a significantly greater risk of laryngeal carcinoma among heavy smokers (P=0.04). The results suggest that smoking plays an important role in the occurrence and development of laryngeal squamous carcinoma; CYP1A1 and MMP9 might be susceptibility gene SNPs for smoking-related laryngeal carcinoma, and ERCC1 might play an important role in heavy smokers. The results of this study might help identify an early marker for the detection and prevention of laryngeal carcinoma.
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Affiliation(s)
- Yi Zhu
- Department of Radiation Oncology of Shanghai Eye and ENT Hospital of Fudan University, Shanghai, 200031, China
| | - Luo Guo
- Department of Experiment centre of Shanghai Eye and ENT Hospital of Fudan University, Shanghai,200031, China
| | - ShengZi Wang
- Department of Radiation Oncology of Shanghai Eye and ENT Hospital of Fudan University, Shanghai, 200031, China
| | - Qun Yu
- Department of TianPing health service centre of Shanghai,Shanghai,200031,China
| | - JianXiong Lu
- Department of TianPing health service centre of Shanghai,Shanghai,200031,China
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Shin KM, Hong MJ, Lee SY, Jin CC, Baek SA, Lee JH, Choi JE, Kang HG, Lee WK, Seok Y, Lee EB, Jeong JY, Yoo SS, Lee J, Cha SI, Kim CH, Kim YC, Oh IJ, Na KJ, Cho S, Jheon S, Park JY. Regulatory variants in cancer-related pathway genes predict survival of patients with surgically resected non-small cell lung cancer. Gene 2017; 646:56-63. [PMID: 29289609 DOI: 10.1016/j.gene.2017.12.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/20/2017] [Accepted: 12/27/2017] [Indexed: 01/11/2023]
Abstract
BACKGROUND We conducted this study to identify genetic variants in cancer-related pathway genes which can predict prognosis of NSCLC patients after surgery, using a comprehensive list of regulatory single nucleotide polymorphisms (SNPs) prioritized by RegulomeDB. METHOD A total of 509 potentially functional SNPs in cancer-related pathway genes selected from RegulomeDB were evaluated. These SNPs were analyzed in a discovery set (n=354), and a replication study was performed in an independent set (n=772). The association of the SNPs with overall survival (OS) and disease-free survival (DFS) were analyzed. RESULTS In the discovery set, 76 SNPs were significantly associated with OS or DFS. Among the 76 SNPs, the association was consistently observed for 5 SNPs (ERCC1 rs2298881C>A, BRCA2 rs3092989G>A, NELFE rs440454C>T, PPP2R4 rs2541164G>A, and LTBP4 rs3786527G>A) in the validation set. In combined analysis, ERCC1 rs2298881C>A, BRCA2 rs3092989, NELFE rs440454C>T, and PPP2R4 rs2541164G>A were significantly associated with OS and DFS (adjusted HR ·aHR· for OS=1.46, 0.62, 078, and 0.76, respectively; P=0.003, 0.002, 0.007, and 0.003 respectively; and aHR for DFS=1.27, 0.69, 0.86, and 0.82, respectively; P=0.02, 0.002, 0.03, and 0.008, respectively). The LTBP4 rs3786527G>A was significantly associated with better OS (aHR=0.75; P=0.003). CONCLUSION Our results suggest that five SNPs in the cancer-related pathway genes may be useful for the prediction of the prognosis in patients with surgically resected NSCLC.
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Affiliation(s)
- Kyung Min Shin
- Department of Radiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Cheng Cheng Jin
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sun Ah Baek
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyo-Gyoung Kang
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won Kee Lee
- Biostatistics, Medical Research Collaboration Center in Kyungpook National University Hospital and Kyungpook National University School of Medicine, Daegu, Korea
| | - Yangki Seok
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea; Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eung Bae Lee
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea; Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Yun Jeong
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Young Chul Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - In Jae Oh
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Kook Joo Na
- Department of Thoracic and Cardiovascular Surgery, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Sanghoon Jheon
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Jae Yong Park
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
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MAPK and ERK polymorphisms are associated with PCOS risk in Chinese women. Oncotarget 2017; 8:100261-100268. [PMID: 29245975 PMCID: PMC5725017 DOI: 10.18632/oncotarget.22153] [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: 06/03/2017] [Accepted: 10/02/2017] [Indexed: 12/24/2022] Open
Abstract
In this case-control study, we analyzed the association between eight RegulomeDB-annotated single nucleotide polymorphisms (SNPs) in the MEK1, MEK2, ERK1 and ERK2 genes and polycystic ovarian syndrome (PCOS). Logistic regression analysis demonstrated that MEK1 rs12050732 (OR = 1.29 [95%CI: 1.06-1.58], P = 0.012), ERK2 rs2266966 (OR = 0.81 [95%CI: 0.67-0.99], P = 0.040) and ERK2 rs5999521 (OR = 0.66 [95%CI: 0.51-0.86], P = 0.002) were associated with PCOS risk without adjusting for age and body mass index. Moreover, PCOS risk increased with allele dosage when these three polymorphisms were combined (Ptrend = 0.001). These findings suggest that genetic variants in key MAPK and ERK genes contribute to PCOS risk in Chinese women.
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Polymorphism in ERCC1 confers susceptibility of coronary artery disease and severity of coronary artery atherosclerosis in a Chinese Han population. Sci Rep 2017; 7:6407. [PMID: 28743890 PMCID: PMC5526898 DOI: 10.1038/s41598-017-06732-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/15/2017] [Indexed: 11/08/2022] Open
Abstract
Excision repair cross-complementing 1 (ERCC1) gene encodes ERCC1 protein, which is mainly responsible for the repair of DNA damage in different diseases including coronary artery atherosclerosis by acting as a rate-limiting element in nucleotide excision repair (NER). Using a three-stage case-control study with 3037 coronary artery disease (CAD) patients and 3002 controls, we investigated associations of three single nucleotide polymorphisms (SNPs) with CAD risk and severity of coronary artery atherosclerosis in Chinese Han population. In the discovery set, the variant allele T of rs11615 was significantly associated with higher CAD risk (adjusted OR = 1.27, P = 0.006) and severity of coronary artery atherosclerosis (adjusted OR = 1.54, P = 0.003). These associations were more remarkable in the merged set (adjusted OR = 1.23, P = 8 × 10-6 for CAD risk; adjusted OR = 1.36, P = 4.3 × 10-5 for severity of coronary artery atherosclerosis). And the expression level of ERCC1 was significantly higher in CAD cases than controls. Multiplicative interactions among SNP rs11615, alcohol drinking, history of T2DM, and history of hyperlipidemia could increase 5.06-fold risk of CAD (P = 1.59 × 10-9). No significant association of rs2298881 and rs3212986 with CAD risk was identified. Taken together, SNP rs11615 in ERCC1 gene might confer susceptibility to CAD and severity of coronary atherosclerosis in a Chinese Han population.
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A practical guide to filtering and prioritizing genetic variants. Biotechniques 2017; 62:18-30. [PMID: 28118812 DOI: 10.2144/000114492] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 10/11/2016] [Indexed: 11/23/2022] Open
Abstract
Next-generation sequencing (NGS) of whole genomes and exomes is a powerful tool in biomedical research and clinical diagnostics. However, the vast amount of data produced by NGS introduces new challenges and opportunities, many of which require novel computational and theoretical approaches when it comes to identifying the causal variant(s) for a disease of interest. While workflows and associated software to process raw data and produce high-confidence variant calls have significantly improved, filtering tens of thousands of candidates to identify a subset relevant to a specific study is still a complex exercise best left to bioinformaticists. However, as this prioritization procedure requires biological/biomedical reasoning, biologists and clinicians are increasingly motivated to handle the task themselves. Here, we describe a set of guidelines, tools, and online resources that can be used to identify functional variants from whole-genome and whole-exome variant calls and then prioritize these variants with potential associations to phenotypes of interest. Insights gained from a recently published analysis of protein-coding gene variation in >60,000 humans by the Exome Aggregation Consortium (ExAC) are also taken into account.
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Wang L, Li G, Liu N, Wang Z, Xu X, Qi J, Ren D, Zhang P, Zhang Y, Tu Y. Genetic variants of SOX9 contribute to susceptibility of gliomas among Chinese population. Oncotarget 2016; 7:65916-65922. [PMID: 27589569 PMCID: PMC5323202 DOI: 10.18632/oncotarget.11679] [Citation(s) in RCA: 2] [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: 06/17/2016] [Accepted: 08/15/2016] [Indexed: 01/08/2023] Open
Abstract
Gliomas make up about 80% of all malignant brain tumors, and cause serious public health problem. Genetic factors and environmental factors jointly caused the development of gliomas, and understanding of the genetic basis is a key component of preventive oncology. However, most genetic factors underlying carcinogenesis of gliomas remain largely unclear. In current study, we systematically evaluated whether genetic variants of SOX9 gene, a transcription factor that plays a central role in the development and differentiation of tumors, contribute to susceptibility of gliomas among Chinese population using a two-stage, case-control study. Results showed that SOX9 rs1042667 was significant associated with increased gliomas risk after adjusted by age, gender, family history of cancer, smoking status and alcohol status (Allele C vs A: OR=1.25; 95% CI=1.11-1.40; P=1.2×10-4). Compared with the carriers of genotype AA, both those of genotype AC (OR=1.37; 95% CI=1.13-1.66) and CC (OR=1.53; 95% CI=1.22-1.91) had significantly increased gliomas risk. This should be the first genetic association study which aims to evaluated the association between genetic variants of SOX9 and susceptibility of gliomas. Additional functional and association studies with different ethnic groups included are needed to further confirm our results.
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Affiliation(s)
- Liang Wang
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Gang Li
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Nan Liu
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Zhen Wang
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Xiaoshan Xu
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Jing Qi
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Dongni Ren
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Pengxing Zhang
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Yongsheng Zhang
- Department of Administrative, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Yanyang Tu
- Department of Experimental Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
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