1
|
Bettim CA, da Silva AV, Kahmann A, Dorn M, Alho CS, Avila E. MC1R and age heteroclassification of face phenotypes in the Rio Grande do Sul population. Int J Legal Med 2024; 138:859-872. [PMID: 38087053 DOI: 10.1007/s00414-023-03143-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/22/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND Forensic DNA phenotyping (FDP) consists of the use of methodologies for predicting externally visible characteristics (EVCs) from the genetic material of biological samples found in crime scenes and has proven to be a promising tool in aiding human identification in police activities. Currently, methods based on multiplex assays and statistical models of prediction of EVCs related to hair, skin, and iris pigmentation using panels of SNP and INDEL biomarkers have already been developed and validated by the forensic scientific community. As well as traces of pigmentation, an individual's perceived age (PA) can also be considered an EVC and its estimation in unknown individuals can be useful for the progress of investigations. Liu and colleagues (2016) were pioneers in evidencing that, in addition to lifestyle and environmental factors, the presence of SNP and INDEL variants in the MC1R gene - which encodes a transmembrane receptor responsible for regulating melanin production - seems to contribute to an individual's PA. The group highlighted the association between these MC1R gene polymorphisms and the PA in the European population, where carriers of risk haplotypes appeared to be up to 2 years older in comparison to their chronological age (CA). PURPOSE Understanding that genotype-phenotype relationships cannot be extrapolated between different population groups, this study aimed to test this hypothesis and verify the applicability of this variant panel in the Rio Grande do Sul admixed population. METHODS Based on genomic data from a sample of 261 volunteers representative of gaucho population and using a multiple linear regression (MLR) model, our group was able to verify a significant association among nine intronic variants in loci adjacent to MC1R (e.g., AFG3L1P, TUBB3, FANCA) and facial age appearance, whose PA was defined after age heteroclassification of standard frontal face images through 11 assessors. RESULTS Different from that observed in European populations, our results show that the presence of effect alleles (R) of the selected variants in our sample influenced both younger and older face phenotypes. The influence of each variant on PA is expressed as β values. CONCLUSIONS There are important molecular mechanisms behind the effects of MC1R locus on PA, and the genomic background of each population seems to be crucial to determine this influence.
Collapse
Affiliation(s)
- Cássio Augusto Bettim
- Structural Bioinformatics and Computational Biology Lab, Institute of Informatics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
| | - Alexsandro Vasconcellos da Silva
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- Technical Scientific and Identification Sections, Superintendency of Federal Police in Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alessandro Kahmann
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil.
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil.
- Interdisciplinary Department, Federal University of Rio Grande Do Sul, Tramandaí, RS, Brazil.
| | - Márcio Dorn
- Structural Bioinformatics and Computational Biology Lab, Institute of Informatics, Federal University of Rio Grande Do Sul, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil
| | - Clarice Sampaio Alho
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil
| | - Eduardo Avila
- National Science and Technology Institute for Forensic Science, Porto Alegre, RS, Brazil
- Technical Scientific and Identification Sections, Superintendency of Federal Police in Rio Grande do Sul, Porto Alegre, RS, Brazil
- National Science and Technology Institute for Children Cancer Biology and Pediatric Oncology, Porto Alegre, RS, Brazil
| |
Collapse
|
2
|
Cheng F, Cui Z, Li Q, Chen S, Li W, Zhang Y. Influence of genetic polymorphisms on imatinib concentration and therapeutic response in patients with chronic-phase chronic myeloid leukemia. Int Immunopharmacol 2024; 133:112090. [PMID: 38640718 DOI: 10.1016/j.intimp.2024.112090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND Diminished bioavailability of imatinib in leukemic cells contributes to poor clinical response. We examined the impact of genetic polymorphisms of imatinib on the pharmacokinetics and clinical response in 190 patients with chronic myeloid leukaemia (CML). METHODS Single nucleotide polymorphisms were genotyped using pyrophosphate sequencing. Plasma trough levels of imatinib were measured using liquid chromatography-tandem mass spectrometry. RESULTS Patients carrying the TT genotype for ABCB1 (rs1045642, rs2032582, and rs1128503), GG genotype for CYP3A5-rs776746 and AA genotype for ABCG2-rs2231142 polymorphisms showed higher concentration of imatinib. Patients with T allele for ABCB1 (rs1045642, rs2032582, and rs1128503), A allele for ABCG2-rs2231142, and G allele for CYP3A5-rs776746 polymorphisms showed better cytogenetic response and molecular response. In multivariate analysis, carriers of the CYP3A5-rs776746 G allele exhibited higher rates of complete cytogenetic response (CCyR) and major molecular response (MMR). Similarly, patients with the T allele of ABCB1-rs1045642 and rs1128503 demonstrated significantly increased CCyR rates. Patients with the A allele of ABCG2-rs2231142 were associated with higher MMR rates. The AA genotype for CYP3A5-rs776746, and the CC genotype for ABCB1-rs104562, and rs1128503 polymorphisms were associated with a higher risk of imatinib failure. Patients with the G allele for CYP3A5-rs776746 exhibited a higher incidence of anemia, and T allele for ABCB1-rs2032582 demonstrated an increased incidence of diarrhea. CONCLUSIONS Genotyping of ABCB1, ABCG2, and CYP3A5 genes may be considered in the management of patients with CML to tailor therapy and optimize clinical outcomes.
Collapse
Affiliation(s)
- Fang Cheng
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China
| | - Zheng Cui
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China
| | - Qiang Li
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China
| | - Shi Chen
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China.
| | - Weiming Li
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Yu Zhang
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan 430022, China.
| |
Collapse
|
3
|
Li Y, Yang Z. The causal effect of exposure to air pollution on risk of adverse pregnancy outcomes: A two-sample Mendelian randomisation study. Sci Total Environ 2024; 928:172234. [PMID: 38615756 DOI: 10.1016/j.scitotenv.2024.172234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/10/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Epidemiological studies have examined the relation between air pollution (NOx, NO2, PM2.5, PM2.5-10, and PM10) and adverse pregnancy outcomes (APOs). There's increasing evidence that air pollution increases the risk of APOs. However, the results of these studies are controversial, and the causal relation remains uncertain. We aimed to assess whether a genetic causal link exists between air pollution and APOs and the potential effects of this relation. METHODS A novel two-sample Mendelian randomisation (MR) study used pooled data from a large-scale complete genome correlation study. The primary analysis method was inverse variance weighting (IVW), which explored the expose-outcome relationship for assessing single nucleotide polymorphisms (SNPs) associated with air pollution. Further sensitivity analysis, including MR-PRESSO, MR-Egger regression, and leave-one analysis, was used to test the consistency of the results. RESULTS There was a significant correlation between air pollution-related SNPs and APOs. A robust causal link was found between genetic susceptibility to air pollution and APOs. CONCLUSIONS Our MR analysis reveals a genetic causal relation between air pollution and APOs, which may help provide new insights into further mechanisms and clinical studies in air pollution-mediated APOs.
Collapse
Affiliation(s)
- Yanhui Li
- Department of Obstetrics and Gynecology, Shandong University Qilu Hospital, 107 Wenhua West Road, Lixia District, Jinan City, Shandong Province, China.
| | - Zhou Yang
- Department of Obstetrics and Gynecology, Shandong University Qilu Hospital, 107 Wenhua West Road, Lixia District, Jinan City, Shandong Province, China
| |
Collapse
|
4
|
Schmidt DA, Galbreath KE, Russello MA. Phylogenomics of American pika (Ochotona princeps) lineage diversification. Mol Phylogenet Evol 2024; 193:108030. [PMID: 38341008 DOI: 10.1016/j.ympev.2024.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Quaternary climate oscillations have profoundly influenced current species distributions. For many montane species, these fluctuations were a prominent driver in species range shifts, often resulting in intraspecific diversification, as has been the case for American pikas (Ochotona princeps). Range shifts and population declines in this thermally-sensitive lagomorph have been linked to historical and contemporary environmental changes across its western North American range, with previous research reconstructing five mitochondrial DNA lineages. Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of O. princeps monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81 mya), including a new Central Rocky Mountain lineage. We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on O. princeps lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.
Collapse
Affiliation(s)
- Danielle A Schmidt
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada.
| |
Collapse
|
5
|
Montenegro AFL, Clementino MAF, Yaochite JNU. Type I interferon pathway genetic variants in severe COVID-19. Virus Res 2024; 342:199339. [PMID: 38354910 PMCID: PMC10901847 DOI: 10.1016/j.virusres.2024.199339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Coronavirus Disease 2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. According to the World Health Organization (WHO), there have been over 760 million reported cases and over 6 million deaths caused by this disease worldwide. The severity of COVID-19 is based on symptoms presented by the patient and is divided as asymptomatic, mild, moderate, severe, and critical. The manifestations are interconnected with genetic variations. The innate immunity is the quickest response mechanism of an organism against viruses. Type I interferon pathway plays a key role in antiviral responses due to viral replication inhibition in infected cells and adaptive immunity stimulation induced by interferon molecules. Thus, variants in type I interferon pathway's genes are being studied in different COVID-19 manifestations. This review summarizes the role of variants in type I interferon pathway's genes on prognosis and severity progression of COVID-19.
Collapse
Affiliation(s)
- A F L Montenegro
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil
| | - M A F Clementino
- Laboratório de Toxinologia Molecular, NUBIMED - Núcleo de Biomedicina, Universidade Federal do Ceará - UFC. Fortaleza, Ceará, Brasil
| | - J N U Yaochite
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil.
| |
Collapse
|
6
|
Zhao F, Shen G, Ren D, Wang M, Liu Z, Zhao Y, Xie Q, Liu Z, Li Z, Gao L, Zhao J. Screening Single Nucleotide Polymorphisms Predicting the Efficacy of Electroacupuncture for Fatigue Treatment in Patients with Breast Cancer Following Adjuvant Chemotherapy. Biochem Genet 2024; 62:1291-1303. [PMID: 37596508 DOI: 10.1007/s10528-023-10477-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/31/2023] [Indexed: 08/20/2023]
Abstract
Chemotherapy-induced fatigue reduces not only the quality of life of patients but also effect their recurrence-free survival rate. Although electroacupuncture can relieve fatigue, it has limited affect on some patients. Therefore, appropriate biomarkers are needed to help screen patients who can benefit from electroacupuncture treatment of fatigue. We conducted this study to explore the predictive ability of SNPs on the efficacy of electroacupuncture in the treatment of fatigue in patients with breast cancer after adjuvant chemotherapy. Our study included breast cancer patients with fatigue after receiving paclitaxel and/or anthracycline based adjuvant chemotherapy. The patients were divided into the electroacupuncture group and the control group. The electroacupuncture treatment group received adjuvant chemotherapy and electroacupuncture treatment, while the control group only received adjuvant chemotherapy, and then compared the fatigue relief degree of two groups. In addition, we used NCBI dbSNP and PharmGKB databases to select fatigue related genes and their SNPs. We collected peripheral blood from the included patients for SNPs typing, and recorded the efficacy of electroacupuncture to analyzed the correlation between different SNPs and therapeutic efficacy. The side effects of electroacupuncture treatment were also recorded. 76 patients in the electroacupuncture group and 48 patients in the control group were enrolled. In the electroacupuncture group, 63 patients (82.9%) experienced moderate to severe fatigue (BFI score > 3). After electroacupuncture treatment, the number of patients with a BFI score of > 3 was 46 (60.5%). Therefore, the fatigue symptoms of 26.9% patients were significantly improved (P < 0.05). In the control group, which did not receive electroacupuncture treatment, 40 of 48 patients had a BFI score of > 3. Following the same observation time used in the electroacupuncture group, 36 patients had a BFI score of > 3 points. Thus, fatigue was not significantly relieved in the control group (83.3% vs. 75.0%, P > 0.05). We included 56 patients in our analysis of the correlation between SNPs and electroacupuncture treatment effects. We divided the patients into an effective group and ineffective group according to therapeutic effects. Our results indicated that the effective rate of electroacupuncture treatment with IL1A rs3783550 AC and CC genotypes was higher than that with other genotypes (AC: 84.6%, CC: 81.8%, AA: 33.0%, P < 0.05). Similarly, the effective rate of electroacupuncture treatment with HTR1A rs6295 GG and CC genotypes was higher than that with other genotypes (GG: 63.0%, CC: 55.6%, GC: 18.2%, P < 0.05). However, no other genotypes were related to the effect of electroacupuncture treatment on fatigue. Our result showed that electroacupuncture has therapeutic effect on fatigue after adjuvant chemotherapy for breast cancer and the side effects are tolerable. In addition, IL1A rs3763550 and HTR1A rss6295 can predict the therapeutic effect of electroacupuncture on fatigue after adjuvant chemotherapy in breast cancer, which helps to better screen patients who can benefit from electroacupuncture treatment.
Collapse
Affiliation(s)
- Fuxing Zhao
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Guoshuang Shen
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Dengfeng Ren
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Miaozhou Wang
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Zhen Liu
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Yi Zhao
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Qiqi Xie
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Zhilin Liu
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Zitao Li
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China
| | - Lihong Gao
- The Fifth People's Hospital of Qinghai Province, The First Ward of Oncology, Xining, 810000, China
| | - Jiuda Zhao
- Breast Disease Diagnosis and Treatment Center, Affiliated Hospital of Qinghai University, Affiliated Cancer Hospital of Qinghai University, Xining, People's Republic of China.
| |
Collapse
|
7
|
Shi W, Zhang Q, Lu Y, Liu J, Ma X, Xie Z, Zhang G, Chang M, Tian Y. Association of single nucleotide polymorphisms in ITLN1 gene with ischemic stroke risk in Xi'an population, Shaanxi province. PeerJ 2024; 12:e16934. [PMID: 38529304 PMCID: PMC10962333 DOI: 10.7717/peerj.16934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/22/2024] [Indexed: 03/27/2024] Open
Abstract
Background Ischemic stroke (IS) is the main cause of death and adult disability. However, the pathogenesis of this complicated disease is unknown. The present study aimed to assess the relationship between ITLN1 single nucleotide polymorphisms (SNPs) and the susceptibility to IS in Xi'an population, Shaanxi province. Methods In this study, we designed polymerase chain reaction (PCR) primers located at -3,308 bp upstream of the transcription initiation site within promoter region of the ITLN1 gene. The target fragment was amplified by PCR and identified by agarose gel electrophoresis. Sanger sequencing was then performed in the samples extracted from a cohort comprising 1,272 participants (636 controls and 636 cases), and the obtained sequences were compared with the reference sequences available on the National Center for Biotechnology Information (NCBI) website to detect SNPs in the ITLN1 gene promoter region. Logistic regression analysis was employed to assess the relationship between ITLN1 polymorphisms and IS risk, with adjustments for age and gender. Significant positive results were tested by false-positive report probability (FPRP) and false discovery rate (FDR). The interaction among noteworthy SNPs and their predictive relationship with IS risk were explored using the Multi-Factor Dimensionality Reduction (MDR) software. Results The results of Sanger sequencing were compared with the reference sequences on the NCBI website, and we found 14 SNPs in ITLN1 gene promoter satisfied Hardy-Weinberg equilibrium (HWE). Logistic regression analysis showed that ITLN1 was associated with a decreased risk of IS (rs6427553: Homozygous C/C: adjusted OR: 0.69, 95% CI [0.48-0.97]; Log-additive: adjusted OR: 0.83, 95% CI [0.70-0.98]; rs7411035: Homozygous G/G: adjusted OR: 0.66, 95% CI [0.47-0.94]; Dominant G/T-G/G: adjusted OR: 0.78, 95% CI [0.62-0.98]; Log-additive: adjusted OR: 0.81, 95% CI [0.69-0.96]; rs4656958: Heterozygous G/A: adjusted OR: 0.74, 95% CI [0.59-0.94]; Homozygous A/A: adjusted OR: 0.51, 95% CI [0.31-0.84]; Dominant G/A-A/A: adjusted OR: 0.71, 95% CI [0.57-0.89]; Recessive A/A: adjusted OR: 0.59, 95% CI [0.36-0.96]; Log-additive: adjusted OR: 0.73, 95% CI [0.61-0.88]), especially in people aged less than 60 years and males. Conclusions In short, our study revealed a correlation between ITLN1 variants (rs6427553, rs7411035 and rs4656958) and IS risk in Xi'an population, Shaanxi province, laying a foundation for ITLN1 gene as a potential biomarker for predicting susceptibility to IS.
Collapse
Affiliation(s)
- Wenzhen Shi
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Qi Zhang
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Ying Lu
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Jie Liu
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Xiaojuan Ma
- Clinical Medical Research Center, Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Zhen Xie
- Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, The College of Life Sciences and Medicine, Northwest University, Xi’an, China
| | - Gejuan Zhang
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Mingze Chang
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| | - Ye Tian
- Department of Neurology, the Affiliated Hospital of Northwest University, Xi’an No.3 Hospital, Xi’an, China
| |
Collapse
|
8
|
Wu SX, Zeng QF, Han WT, Wang MY, Ding H, Teng MX, Wang MY, Li PY, Gao X, Bao ZM, Wang B, Hu JJ. Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus). Zool Res 2024; 45:329-340. [PMID: 38485503 PMCID: PMC11017084 DOI: 10.24272/j.issn.2095-8137.2023.270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.
Collapse
Affiliation(s)
- Shao-Xuan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Qi-Fan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China
| | - Wen-Tao Han
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Meng-Ya Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Hui Ding
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Ming-Xuan Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Ming-Yi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Pei-Yu Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Xin Gao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Zhen-Min Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Bo Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China. E-mail:
| | - Jing-Jie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou, Guangdong 511458, China. E-mail:
| |
Collapse
|
9
|
El-Sayed A, Refaai M, Ateya A. Doppler ultrasonographic scan, gene expression and serum profile of immune, APPs and antioxidant markers in Egyptian buffalo-cows with clinical endometritis. Sci Rep 2024; 14:5698. [PMID: 38459095 PMCID: PMC10923904 DOI: 10.1038/s41598-024-56258-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
The objective of this study was to elaborate Doppler ultrasonographic scan, genetic resistance and serum profile of markers associated with endometritis susceptibility in Egyptian buffalo-cows. The enrolled animals were designed as; twenty five apparently healthy buffalo-cows considered as a control group and twenty five infected buffalo with endometritis. There were significant (p < 0.05) increased of cervical diameter, endometrium thickness, uterine horn diameter, TAMEAN, TAMAX and blood flow through middle uterine artery with significant decrease of PI and RI values in endometritis buffalo-cows. Gene expression levels were considerably higher in endometritis-affected buffaloes than in resistant ones for the genes A2M, ADAMTS20, KCNT2, MAP3K4, MAPK14, FKBP5, FCAMR, TLR2, IRAK3, CCl2, EPHA4, and iNOS. The RXFP1, NDUFS5, TGF-β, SOD3, CAT, and GPX genes were expressed at substantially lower levels in endometritis-affected buffaloes. The PCR-DNA sequence verdicts of healthy and affected buffaloes revealed differences in the SNPs in the amplified DNA bases related to endometritis for the investigated genes. However, MAP3K4 elicited a monomorphic pattern. There was a significant decrease of red blood cells (RBCs) count, Hb and packed cell volume (PCV) with neutrophilia, lymphocytosis and monocytosis in endometritis group compared with healthy ones. The serum levels of Hp, SAA, Cp, IL-6, IL-10, TNF-α, NO and MDA were significantly (P˂0.05) increased, along with reduction of CAT, GPx, SOD and TAC in buffalo-cows with endometritis compared to healthy ones. The variability of Doppler ultrasonographic scan and studied genes alongside alterations in the serum profile of investigated markers could be a reference guide for limiting buffalo endometritis through selective breeding of natural resistant animals.
Collapse
Affiliation(s)
- Ahmed El-Sayed
- Department of Animal Health and Poultry, Animal and Poultry Production Division, Desert Research Center (DRC), Cairo, Egypt
| | - Mohamed Refaai
- Diagnostic Imaging and Endoscopy Unit, Agriculture Research Centre, Animal Reproduction Research Institute, Giza, Egypt
| | - Ahmed Ateya
- Department of Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
| |
Collapse
|
10
|
Broberg M, Ampuja M, Jones S, Ojala T, Rahkonen O, Kivelä R, Priest J, Palotie A, Ollila HM, Helle E. Genome-wide association studies highlight novel risk loci for septal defects and left-sided congenital heart defects. BMC Genomics 2024; 25:256. [PMID: 38454350 PMCID: PMC10918883 DOI: 10.1186/s12864-024-10172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/28/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Congenital heart defects (CHD) are structural defects of the heart affecting approximately 1% of newborns. They exhibit low penetrance and non-Mendelian patterns of inheritance as varied and complex traits. While genetic factors are known to play an important role in the development of CHD, the specific genetics remain unknown for the majority of patients. To elucidate the underlying genetic risk, we performed a genome wide association study (GWAS) of CHDs in general and specific CHD subgroups using the FinnGen Release 10 (R10) (N > 393,000), followed by functional fine-mapping through eQTL and co-localization analyses using the GTEx database. RESULTS We discovered three genome-wide significant loci associated with general CHD. Two of them were located in chromosome 17: 17q21.32 (rs2316327, intronic: LRRC37A2, Odds ratio (OR) [95% Confidence Interval (CI)] = 1.17[1.12-1.23], p = 1.5 × 10-9) and 17q25.3 (rs1293973611, nearest: BAHCC1, OR[95%CI] = 4.48[2.80-7.17], p = 7.0 × 10-10), respectively, and in addition to general CHD, the rs1293973611 locus was associated with the septal defect subtype. The third locus was in band 1p21.2 (rs35046143, nearest: PALMD, OR[95%CI] = 1.15[1.09-1.21], p = 7.1 × 10-9), and it was associated with general CHD and left-sided lesions. In the subgroup analysis, two additional loci were associated with septal defects (rs75230966 and rs6824295), and one with left-sided lesions (rs1305393195). In the eQTL analysis the variants rs2316327 (general CHD), and rs75230966 (septal defects) both located in 17q21.32 (with a LD r2 of 0.41) were both predicted to significantly associate with the expression of WNT9B in the atrial appendage tissue category. This effect was further confirmed by co-localization analysis, which also implicated WNT3 expression in the atrial appendage. A meta-analysis of general CHD together with the UK Biobank (combined N = 881,678) provided a different genome-wide significant locus in LRRC37A2; rs16941382 (OR[95%CI] = 1.15[1.11-1.20], p = 1.5 × 10-9) which is in significant LD with rs2316327. CONCLUSIONS Our results of general CHD and different CHD subcategories identified a complex risk locus on chromosome 17 near BAHCC1 and LRRC37A2, interacting with the genes WNT9B, WNT3 and MYL4, may constitute potential novel CHD risk associated loci, warranting future experimental tests to determine their role.
Collapse
Affiliation(s)
- Martin Broberg
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Minna Ampuja
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Samuel Jones
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Tiina Ojala
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Otto Rahkonen
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Riikka Kivelä
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Wihuri Research Institute, 00290, Helsinki, Finland
- Faculty of Sport and Health Sciences, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - James Priest
- School of Medicine, Stanford University, Stanford University, Stanford, CA, 94305, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Emmi Helle
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland.
- Department of Pediatric Cardiology, New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00029, Helsinki, Finland.
- , Haartmaninkatu 8, Helsinki, 00014, Finland.
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, 00271, Finland.
| |
Collapse
|
11
|
Wang G, Jing L, Wang Y, Mehmood A, Zhang H, Guo R, Zhang L, Li B. Interferon Regulatory Factor 5 Gene Polymorphisms and mRNA Expression Levels Are Associated with Neuromyelitis Optica Spectrum Disorder. Mol Neurobiol 2024:10.1007/s12035-024-04072-0. [PMID: 38451436 DOI: 10.1007/s12035-024-04072-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/23/2024] [Indexed: 03/08/2024]
Abstract
Interferon regulatory factor 5 (IRF5) is a critical transcription factor in the toll-like receptor signaling pathway. It is associated with autoimmune disorders, such as rheumatoid arthritis, systemic lupus erythematosus, and inflammatory bowel disease. However, the relationship between the functional single nucleotide polymorphisms (SNPs) of IRF5 and its mRNA expression level in patients with neuromyelitis optica spectrum disorder remains unclear. The present study aimed to investigate the relationship between polymorphisms and mRNA expression levels of the IRF5 gene with the incidence of neuromyelitis optica spectrum disorder (NMOSD) in northern Chinese Han people. Two loci of the IRF5 gene (rs2004640 and rs2280714) of 164 patients with NMOSD and 269 healthy subjects were genotyped using the multiple SNaPshot technique. The frequencies of alleles, genotypes, and haplotypes were compared. Stratified analysis was performed according to age, sex, AQP4 status, onset age, and Expanded Disability Status Scale (EDSS) score. The IRF5 mRNA levels in peripheral blood mononuclear cells (PBMCs) of 64 NMOSD patients (32 patients in the acute stage and 32 patients in the remission stage) and 35 healthy subjects were detected by real-time PCR. The association of SNP polymorphisms with the mRNA expression level was determined by nonparametric tests. Allele and genotype frequency distributions of rs2004640 showed significant differences between both groups. Compared to healthy controls, the frequency of rs2004640 T allele markedly increased in patients (OR = 1.51, 95% CI = 1.09-2.08, P = 0.005). Minor allele T and GT genotype of rs2004640 that significantly increases the risk of NMOSD were discovered using genetic inheritance models (codominant, dominant, and overdominant) and haplotype analyses. Subsequent haplotype analyses revealed that the major haplotype "T-A" containing the risk alleles (the SNP sequence of the alleles was rs2004640 and rs2280714) had adverse effects on NMOSD. Based on the stratification analysis according to the EDSS score, the GT genotype frequency in the EDSS ≥ 4 group (38.2%) was markedly lower than that in the EDSS < 4 group (61.8%) (OR = 0.32, 95% CI = 0.15-0.68, P = 0.0054), with a significant difference. The IRF5 mRNA expression level was increased in NMOSD patients compared to that in normal subjects. IRF5 gene polymorphisms may be tightly associated with the genesis and progression of NMOSD in northern Chinese Han people. IRF5 mRNA expression was increased in patients with NMOSD and significantly increased in patients with acute phase. Perhaps IRF5 expression levels can be used as a predictor of disease activity in the future.
Collapse
Affiliation(s)
- Gaoning Wang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China
- Department of Neurology, The First Hospital of Qinhuangdao, Qinhuangdao, Hebei, China
| | - Liu Jing
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China
- Department of Neurology, The First Hospital of Qinhuangdao, Qinhuangdao, Hebei, China
| | - Ying Wang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China
| | - Arshad Mehmood
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China
| | - Huining Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China
| | - Ruoyi Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China
| | - Lu Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China
| | - Bin Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China.
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, China.
| |
Collapse
|
12
|
Ma Z, Wang W, Zhang D, Zhang Y, Zhao Y, Li X, Zhao L, Cheng J, Xu D, Yang X, Liu J, He L, Chen Z, Gong P, Zhang X. Polymorphisms of PLIN1 and MOGAT1 genes and their association with feed efficiency in Hu sheep. Gene 2024; 897:148072. [PMID: 38081333 DOI: 10.1016/j.gene.2023.148072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Feed cost accounts for a high proportion of sheep production, and improving sheep's utilization of feed will reduce production costs and improve economic benefits. The purpose of this study was to investigate the expression characteristics of PLIN1 and MOGAT1 genes and the relationship between their polymorphisms and feed efficiency traits in Hu sheep, and to find molecular Genetic marker that can be used in breeding. The expression levels of PLIN1 and MOGAT1 genes in various tissues were determined using quantitative real-time PCR (qRT-PCR). The results showed that PLIN1 and MOGAT1 genes were widely expressed in heart, liver, spleen, lungs, kidneys, rumen, duodenum, muscle, lymph, and tail fat. The PLIN1 gene had the highest expression level in in the tail fat compared to the other nine tissues. The expression levels of MOGAT1 gene in liver, tail fat, lung and heart was significantly higher than in kidney, muscle and lymph. The expression level of MOGAT1 was lowest in muscle compared to the other tissues (heart, liver, spleen, lung, rumen and tail fat). We recorded the body weight (BW80 and BW180) and feed intake (FI) information of 985 male Hu sheep at 80 and 180 days of age, and calculated the daily average feed intake (ADFI), average daily gain (ADG), and feed conversion rate (FCR) from 80 to 180 days of age. Two intronic mutations, g.18517910 A > G and g.224856118 G > C, were identified in PLIN1 and MOGAT1 genes by PCR amplification and Sanger sequencing. MassARRAY ® SNP detection technology was used to genotype the DNA of 985 Hu sheep and analyze its association with feed efficiency traits. The results showed that the SNP g.18517910 A > G was significantly associated with BW80, BW180, FI, ADFI and FCR (P < 0.05), while SNP g.2248561118 G > C was significantly associated with FCR (P < 0.05). Meanwhile, significant differences were also observed in different combinations of genotypes (P < 0.05). Therefore, these two polymorphic loci can serve as candidate molecular markers for improving feed utilization efficiency in Hu sheep.
Collapse
Affiliation(s)
- Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Xiaolong Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Liming Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou Gansu 730020, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lijuan He
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zhanyu Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Science, Urumqi, 830057, China.
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
| |
Collapse
|
13
|
Jing J, Xu D, Li Z, Wang J, Dai J, Li FS. Genetic variation of six specific SNPs of chronic obstructive pulmonary disease among Chinese population. Pulmonology 2024; 30:113-121. [PMID: 35501282 DOI: 10.1016/j.pulmoe.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a chronic bronchitis (or) emphysema with a high disability and fatality rate. This study aimed to explore the correlation between the six selected single nucleotide polymorphisms (SNPs) and the risk of COPD in the Chinese population. METHODS The Agena MassARRAY platform was used to select six SNPs from 629 subjects for genotyping. The correlation between SNPs and COPD risk was evaluated using calculated odds ratios (ORs) and 95% confidence intervals (CIs). Multi-factor dimensionality reduction (MDR) was performed to analyze the impact of SNP interactions on COPD risk. Multiple comparisons were performed using Bonferroni- correction. RESULTS Our results indicated that rs4719841 and rs7934083 variants were associated with a reduced risk of COPD. The analysis results of age, gender and non-smokers showed that rs4719841 and rs7934083 were associated with reducing the risk of COPD. In addition, the results showed that the genetic models of rs4719841, rs7934083 and rs7780562 were related to the forced vital capacity, respiratory rate per second, and respiratory rate / forced vital capacity of COPD patients, respectively. The results of the MDR analysis showed that the three-locus model (rs4719841, rs7934083, and rs78750958) is the best for COPD risk assessment. CONCLUSION This study shows that rs4719841 and rs7934083 are associated with the risk of COPD in the Chinese population, which provides some insights for early screening, prevention, and diagnosis of COPD in high-risk populations.
Collapse
Affiliation(s)
- J Jing
- The Fourth Clinical Medical College of Xinjiang Medical University, China; The COPD Laboratory of Clinical Research Base, Chinese Medicine Hospital of Xinjiang Uygur Autonomous Region, China
| | - D Xu
- The COPD Laboratory of Clinical Research Base, Chinese Medicine Hospital of Xinjiang Uygur Autonomous Region, China
| | - Z Li
- The COPD Laboratory of Clinical Research Base, Chinese Medicine Hospital of Xinjiang Uygur Autonomous Region, China
| | - J Wang
- The Clinical Research Base Laboratory, Chinese Medicine Hospital of Xinjiang Uygur Autonomous Region, China
| | - J Dai
- The Fourth Clinical Medical College of Xinjiang Medical University, China
| | - F S Li
- The COPD Laboratory of Clinical Research Base, Chinese Medicine Hospital of Xinjiang Uygur Autonomous Region, China; The Clinical Research Base Laboratory, Chinese Medicine Hospital of Xinjiang Uygur Autonomous Region, China.
| |
Collapse
|
14
|
Woerner AE, Crysup B, King JL, Novroski NM, Coble MD. Mixture detection with Demixtify. Forensic Sci Int Genet 2024; 69:102980. [PMID: 38016331 DOI: 10.1016/j.fsigen.2023.102980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023]
Abstract
The de facto genetic markers of forensics are short tandem repeats (STRs). There are many analytical tools designed to work with STRs, including techniques for analyzing and assessing DNA mixtures. In contrast, the nascent field of forensic genetic genealogy often relies on biallelic single nucleotide polymorphisms (SNPs). Tools designed for the forensic assessment of SNPs are somewhat lacking, especially for DNA mixtures. In this paper we introduce Demixtify, a program that detects DNA mixtures using biallelic SNPs. Demixtify is quite powerful; highly imbalanced mixtures can be detected (≤1:99, considering in silico and in vitro mixtures) when coverage is ample. Demixtify can also detect mixtures in low coverage (∼1×) samples (when the mixture is relatively balanced). Demixtify includes an empirical estimator of sequence error that is specific to the markers assayed, making it especially relevant to the forensic community. Orthogonal techniques are also developed to characterize in vitro mixtures, as well as samples thought to be single source, and the results of these approaches serve to validate the techniques presented.
Collapse
Affiliation(s)
- August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science, Center, Fort Worth, TX, USA.
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science, Center, Fort Worth, TX, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Nicole M Novroski
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Michael D Coble
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science, Center, Fort Worth, TX, USA
| |
Collapse
|
15
|
Ikejiri K, Suzuki T, Muto S, Takama H, Yamawaki K, Miyazawa T, Urakawa I, Aoki Y, Otsuki A, Katsuoka F, Kinoshita K, Nangaku M, Akizawa T, Yamamoto M. Effects of NRF2 polymorphisms on safety and efficacy of bardoxolone methyl: subanalysis of TSUBAKI study. Clin Exp Nephrol 2024; 28:225-234. [PMID: 37962746 PMCID: PMC10881689 DOI: 10.1007/s10157-023-02427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND In the TSUBAKI study, bardoxolone methyl significantly increased measured and estimated glomerular filtration rates (GFR) in patients with multiple forms of chronic kidney disease (CKD), including Japanese patients with type 2 diabetes and stage 3-4 CKD. Since bardoxolone methyl targets the nuclear factor erythroid 2-related factor 2 pathway, this exploratory analysis of the TSUBAKI study investigated the impact of the regulatory single nucleotide polymorphism, rs6721961, on the effects of bardoxolone methyl. METHODS Japanese patients aged 20-79 years with type 2 diabetes and stage 3-4 CKD were randomized to bardoxolone methyl 5-15 mg/day (titrated as tolerated) or placebo for 16 weeks. Genotype frequency, clinical characteristics, renal function, and adverse events were primarily assessed. RESULTS Of 104 patients (bardoxolone methyl n = 55, placebo n = 49); 57% were genotype C/C, 32% C/A and 12% A/A. The frequency of the A/A genotype was higher among patients with diabetic kidney disease than in the general Japanese population (~ 5%). Measured and estimated GFRs increased from baseline in all genotypes receiving bardoxolone methyl. There were no significant differences between genotypes for safety parameters, including blood pressure, bodyweight, and levels of B-type natriuretic peptide, or in the type and frequency of adverse events, suggesting that the efficacy and safety of bardoxolone methyl are unaffected by the rs6721961 polymorphism-617 (C→A) genotype. CONCLUSIONS Our approach of combining genome analysis with clinical trials for an investigational drug provides important and useful clues for exploring the efficacy and safety of the drug. TRIAL REGISTRATION ClinicalTrials.gov; NCT02316821.
Collapse
Affiliation(s)
- Kazuaki Ikejiri
- Research and Development Division, Kyowa Kirin Co., Ltd, 1-9-2 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Takafumi Suzuki
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Satsuki Muto
- Research and Development Division, Kyowa Kirin Co., Ltd, 1-9-2 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Hirotaka Takama
- Research and Development Division, Kyowa Kirin Co., Ltd, 1-9-2 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Kengo Yamawaki
- Research and Development Division, Kyowa Kirin Co., Ltd, 1-9-2 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Tatsuya Miyazawa
- Research and Development Division, Kyowa Kirin Co., Ltd, 1-9-2 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Itaru Urakawa
- Research and Development Division, Kyowa Kirin Co., Ltd, 1-9-2 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tadao Akizawa
- Division of Nephrology, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
| |
Collapse
|
16
|
Villikudathil AT, Mc Guigan DH, English A. Exploring metformin monotherapy response in Type-2 diabetes: Computational insights through clinical, genomic, and proteomic markers using machine learning algorithms. Comput Biol Med 2024; 171:108106. [PMID: 38368755 DOI: 10.1016/j.compbiomed.2024.108106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND In 2016, the UK had 4.5 million people with diabetes, predominantly Type-2 Diabetes Mellitus (T2DM). The NHS allocates £10 billion (9% of its budget) to manage diabetes. Metformin is the primary treatment for T2DM, but 35% of patients don't benefit from it, leading to complications. This study aims to delve into metformin's efficacy using clinical, genomic, and proteomic data to uncover new biomarkers and build a Machine Learning predictor for early metformin response detection. METHODS Here we report analysis from a T2DM dataset of individuals prescribed metformin monotherapy from the Diastrat cohort recruited at the Altnagelvin Area Hospital, Northern Ireland. RESULTS In the clinical data analysis, comparing responders (those achieving HbA1c ≤ 48 mmol/mol) to non-responders (with HbA1c > 48 mmol/mol), we identified that creatinine levels and bodyweight were more negatively correlated with response than non-response. In genomic analysis, we identified statistically significant (p-value <0.05) variants rs6551649 (LPHN3), rs6551654 (LPHN3), rs4495065 (LPHN3) and rs7940817 (TRPC6) which appear to differentiate the responders and non-responders. In proteomic analysis, we identified 15 statistically significant (p-value <0.05, q-value <0.05) proteomic markers that differentiate controls, responders, non-responders and treatment groups, out of which the most significant were HAOX1, CCL17 and PAI that had fold change ∼2. A machine learning model was build; the best model predicted non-responders with 83% classification accuracy. CONCLUSION Further testing in prospective validation cohorts is required to determine the clinical utility of the proposed model.
Collapse
Affiliation(s)
- Angelina Thomas Villikudathil
- Ulster University, Centre for Stratified Medicine, Faculty of Life and Health Sciences, Magee Campus, Londonderry, Northern Ireland, United Kingdom.
| | - Declan H Mc Guigan
- Ulster University, Centre for Stratified Medicine, Faculty of Life and Health Sciences, Magee Campus, Londonderry, Northern Ireland, United Kingdom
| | - Andrew English
- School of Health and Life Sciences, Teesside University, England, United Kingdom
| |
Collapse
|
17
|
Zhang F, Zhou P, Wang L, Liao X, Liu X, Ke C, Wen S, Shu Y. Polymorphisms of IFN signaling genes and FOXP4 influence the severity of COVID-19. BMC Infect Dis 2024; 24:270. [PMID: 38429664 PMCID: PMC10905836 DOI: 10.1186/s12879-024-09040-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/20/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The clinical manifestations of COVID-19 range from asymptomatic, mild to moderate, severe, and critical disease. Host genetic variants were recognized to affect the disease severity. However, the genetic landscape differs among various populations. Therefore, we explored the variants associated with COVID-19 severity in the Guangdong population. METHODS A total of 314 subjects were selected, of which the severe and critical COVID-19 patients were defined as "cases", and the mild and moderate patients were defined as "control". Twenty-two variants in interferon-related genes and FOXP4 were genotyped using the MassARRAY technology platform. RESULTS IFN signaling gene MX1 rs17000900 CA + AA genotype was correlated with a reduced risk of severe COVID-19 in males (P = 0.001, OR = 0.050, 95%CI = 0.008-0.316). The AT haplotype comprised of MX1 rs17000900 and rs2071430 was more likely to protect against COVID-19 severity (P = 6.3E-03). FOXP4 rs1886814 CC genotype (P = 0.001, OR = 3.747, 95%CI = 1.746-8.043) and rs2894439 GA + AA genotype (P = 0.001, OR = 5.703, 95% CI = 2.045-15.903) were correlated with increased risk of severe COVID-19. Haplotype CA comprised of rs1886814 and rs2894439 was found to be correlated with adverse outcomes (P = 7.0E-04). FOXP4 rs1886814 CC (P = 0.0004) and rs2894439 GA + AA carriers had higher neutralizing antibody titers (P = 0.0018). The CA + AA genotype of MX1 rs17000900 tended to be correlated with lower neutralizing antibody titers than CC genotype (P = 0.0663), but the difference was not statistically significant. CONCLUSION Our study found a possible association between MX1 and FOXP4 polymorphisms and the severity of COVID-19. Distinguishing high-risk patients who develop severe COVID-19 will provide clues for early intervention and individual treatment strategies.
Collapse
Affiliation(s)
- Feng Zhang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Pingping Zhou
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, P. R. China
| | - Liangliang Wang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Xinzhong Liao
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Xuejie Liu
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, P. R. China
| | - Simin Wen
- Guangzhou First People's Hospital, the Second Affiliated Hospital of South China University of Technology, Guangzhou, P. R. China.
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen, 518107, P. R. China.
- Key Laboratory of Pathogen Infection Prevention and Control (MOE), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, P. R. China.
| |
Collapse
|
18
|
Sharma A, Muthu MS, Vettriselvi V, Nuvvula S, Gayathri T. AMELX gene association to early childhood caries in south-Indian children: a case-control study. Eur Arch Paediatr Dent 2024:10.1007/s40368-024-00866-x. [PMID: 38409576 DOI: 10.1007/s40368-024-00866-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 01/15/2024] [Indexed: 02/28/2024]
Abstract
PURPOSE Genetic variants of AMELX gene can affect the protein content, organization of enamel prisms, microstructure and microhardness of the enamel, thus altering the caries susceptibility. The present study aims to assess the association between polymorphisms rs17878486, rs5934997, and rs5933871 of AMELX gene and Early Childhood Caries (ECC). MATERIALS AND METHODS This case-control study was conducted on 200 participants, aged 3-6 years, with 100 controls and 100 children with ECC. A questionnaire was used to collect demographic data, birth-weight, type of delivery, oral hygiene practices, feeding history and 24-h diet diary. DNA was isolated from blood and subjected to PCR followed by Sanger sequencing. RESULTS The CC genotype of rs17878486 showed an OR of 1.93 (0.34-10.81; P = 0.73). In a recessive model, the CC genotype of rs17878486 reported an OR of 2.04 (0.36-11.40; P = 0.68); rs5593871 reported an OR of 1.00 (0.31-3.21). Statistically significant differences (P ≤ 0.05) between genotype and allele frequencies of rs17878486, rs5934997, and rs5933871 were not observed between children with ECC and the controls. CONCLUSION Polymorphisms of AMELX gene did not show a significant association with ECC in this population. However, documentation of genetic data in a global context of ECC may be essential for the future.
Collapse
Affiliation(s)
- A Sharma
- Centre for Early Childhood Caries Research (CECCRe), Department of Pediatric and Preventive Dentistry, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
- Department of Pediatric and Preventive Dentistry, Indira Gandhi Institute of Dental Sciences, Sri Balaji Vidyapeeth, Pillayarkuppam, Pondicherry, India
| | - M S Muthu
- Centre for Early Childhood Caries Research (CECCRe), Department of Pediatric and Preventive Dentistry, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - V Vettriselvi
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - S Nuvvula
- Department of Pediatric and Preventive Dentistry, Narayana Dental College and Hospital, Nellore, India
| | - T Gayathri
- Faculty of Allied Health Sciences, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| |
Collapse
|
19
|
Wang Z, Sun Y. Unraveling the causality between chronic obstructive pulmonary disease and its common comorbidities using bidirectional Mendelian randomization. Eur J Med Res 2024; 29:143. [PMID: 38403592 PMCID: PMC10895842 DOI: 10.1186/s40001-024-01686-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) frequently coexists with various diseases, yet the causal relationship between COPD and these comorbidities remains ambiguous. As a result, the aim of our study is to elucidate the potential causality between COPD and its common comorbidities. METHODS We employed the Mendelian randomization (MR) method to analyze single nucleotide polymorphism (SNP) data of common comorbidities with COPD from FinnGen and Integrative Epidemiology Unit (IEU) databases. Causality was primarily assessed using the inverse variance weighting (IVW) method. Multivariable Mendelian randomization (MVMR) analysis was also conducted to eliminate the interference of smoking-related phenotypes. Sensitivity analysis was conducted to ensure the reliability of our findings. RESULTS Preliminary univariable MR revealed an increased risk of lung squamous cell carcinoma (LUSC) (IVW: OR = 1.757, 95% CI = 1.162-2.657, P = 0.008), chronic kidney disease (CKD) (IVW: OR = 1.193, 95% CI = 1.072-1.326, P < 0.001), chronic periodontitis (IVW: OR = 1.213, 95% CI = 1.038-1.417, P = 0.012), and heart failure (HF) (IVW: OR = 1.127, 95% CI = 1.043-1.218, P = 0.002). Additionally, the reverse MR analysis indicated that genetic susceptibility to HF (IVW: OR = 1.272, 95% CI = 1.084-1.493, P = 0.003), obesity (IVW: OR = 1.128, 95% CI = 1.056-1.205, P < 0.001), depression (IVW: OR = 1.491, 95% CI = 1.257-1.770, P < 0.001), and sleep apnea syndrome (IVW: OR = 1.209, 95% CI = 1.087-1.345, P < 0.001) could raise the risk of COPD. The MVMR analysis showed no causal effect of COPD on susceptibility to chronic periodontitis after adjusting for smoking. CONCLUSIONS Our study identified that COPD may elevate the risk of LUSC, HF, and CKD. Additionally, our analysis revealed that HF, sleep apnea symptoms, depression, and obesity might also increase the susceptibility to COPD. These findings revealed a potential causal relationship between COPD and several prevalent comorbidities, which may provide new insights for disease early prediction and prevention.
Collapse
Affiliation(s)
- Zihan Wang
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital; Research Center for Chronic Airway Diseases, Peking University Health Science Center, Beijing, China
| | - Yongchang Sun
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital; Research Center for Chronic Airway Diseases, Peking University Health Science Center, Beijing, China.
| |
Collapse
|
20
|
Chermon D, Birk R. Brain-derived neurotrophic factor gene rs925946 associates with Israeli females' obesity predisposition: An interaction between genetics, eating habits, and physical inactivity. Nutr Res 2024; 125:61-68. [PMID: 38503023 DOI: 10.1016/j.nutres.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/21/2024]
Abstract
The global obesity pandemic presents a pressing health challenge, with an increasing prevalence shaped by an intricate interplay of genetics and environment. Brain-derived neurotrophic factor (BDNF) plays a pivotal role in regulating feeding behavior and energy expenditure. BDNF single nucleotide polymorphisms have been linked to obesity risk. We hypothesized that BDNF rs925946 is positively associated with obesity susceptibility in the Israeli population. We aimed to study BDNF rs925946 association with obesity susceptibility and its interaction with environmental factors, including eating habits, sugar-sweetened beverages, and physical activity. A data cohort of 4668 Israeli adults (≥18 years, Jewish) was analyzed. Participants' genotypic data for the BDNF rs925946 and lifestyle and eating behavior questionnaire data were analyzed for the association between obesity predisposition and gene-environment interactions. Female (n = 3259) BDNF rs925946 T-allele carriers had an elevated obesity odd (odds ratio [OR] = 1.2; 95% confidence interval [CI], 1.03-1.4, P = .02). BDNF rs925946 genotype interacted significantly with physical inactivity, sugar-sweetened beverage consumption, and eating habits score to enhance obesity odds (OR = 1.4; 95% CI, 1.14-1.7; OR = 1.54, 95% CI, 1.1-2.15; and OR = 1.4; 95% CI, 1.2-2.11, respectively). Our data demonstrated a significant association between BDNF rs925946 T-allele female carriers and a higher obesity predisposition, affected by modifiable lifestyle factors.
Collapse
Affiliation(s)
- Danyel Chermon
- Nutrition Department, Health Sciences Faculty, Ariel University, 407000, Israel
| | - Ruth Birk
- Nutrition Department, Health Sciences Faculty, Ariel University, 407000, Israel.
| |
Collapse
|
21
|
Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED. An atlas of protein homo-oligomerization across domains of life. Cell 2024; 187:999-1010.e15. [PMID: 38325366 DOI: 10.1016/j.cell.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
Collapse
Affiliation(s)
- Hugo Schweke
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tal Levin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Prasun Kumar
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Yoan Duhoo
- Protein Production and Structure Characterization Core Facility (PTPSP), School of Life Sciences, École polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benjamin Dubreuil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sucharita Dey
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, India.
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
22
|
Zhang Y, Zhao K, Jin L, Zhou Y, Shang X, Wang X, Yu H. MTNR1B gene variations and high pre-pregnancy BMI increase gestational diabetes mellitus risk in Chinese women. Gene 2024; 894:148023. [PMID: 38007162 DOI: 10.1016/j.gene.2023.148023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/08/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
AIM To investigate the association of melatonin receptor 1B (MTNR1B) gene variations and pre-pregnancy body mass index (BMI) with gestational diabetes mellitus (GDM). MATERIALS AND METHOD In this study, 1566 Chinese Han pregnant women were enrolled and multiple genetic models were used to evaluate the association between MTNR1B gene polymorphisms and the risk of GDM. The clinical value of pre-pregnancy BMI in predicting GDM was analyzed and evaluated using receiver operating characteristic (ROC) curves. Several methods of analysis were used to examine the impact of gene-gene and gene-BMI interactions on the incidence of GDM influence. RESULTS For the MTNR1B gene, rs1387153 (C > T), rs10830962 (C > G), rs4753426 (T > C), and rs10830963 (C > G) are all risk mutations associated with the susceptibility of GDM. The ROC curve analysis indicated that the BMI demonstrated an area under the curve (AUC) of 0.595. Alongside, the sensitivity and specificity stood at 0.676 and 0.474 respectively. The maximum Joden index was found to be 0.150, with a corresponding critical BMI value of 20.5691 kg/m2. Interaction analysis revealed that gene-gene and gene-BMI interactions had no significant effect on GDM occurrence. CONCLUSION MTNR1B genetic variations confers the risk to GDM in Chinese women. Furthermore, the high pre-pregnancy BMI (≥20.5691 kg/m2) significantly increases the risk of GDM in Chinese women.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Guizhou, China
| | - Kai Zhao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Jin
- Institute of Reproductive and Child Health, National Health Commission Key Laboratory of Reproductive Health, Peking University, Beijing, China
| | - Yuanzhong Zhou
- School of Public health, Key Laboratory of Maternal & Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi Medical University, Guizhou, China
| | - Xuejun Shang
- Department of Urology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China.
| | - Xin Wang
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Guizhou, China.
| | - Hongsong Yu
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Guizhou, China.
| |
Collapse
|
23
|
Wang B, Xiong Y, Li R, Zhang S. Potential role of SNP rs2071475 in rheumatoid arthritis and inflammatory bowel disease in the East Asian population: a Mendelian randomization study. Inflammopharmacology 2024; 32:683-692. [PMID: 37855981 PMCID: PMC10907428 DOI: 10.1007/s10787-023-01363-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/01/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Previous observational studies have identified an association between rheumatoid arthritis (RA) and inflammatory bowel disease (IBD). However, the causal relationship between RA and IBD in the East Asian population remains uncertain. METHODS The two-sample Mendelian randomization (MR) analysis was conducted to elucidate the potential causal relationship between RA and IBD. Summary-level data from genome-wide association studies (GWAS) in the East Asian population were utilized, including RA (n = 19,190) and IBD (n = 6543), including Crohn's disease (CD, n = 5409) and ulcerative colitis (UC, n = 4853). The inverse variance weighted (IVW) method was employed as the primary analysis, supplemented by weighted median, weighted mode, simple median, MR-Egger, and MR-PRESSO analyses. Sensitivity analyses were conducted to assess the robustness of the results. Genetic data for RA (n = 22,515) were utilized to validate the findings in the East Asian population. RESULTS The IVW method showed no significant association between genetically predicted RA and overall IBD in the East Asian population (OR = 1.028; 95% CI: 0.935-1.129; P = 0.567). The subgroup analysis revealed a positive association between RA and CD (OR = 1.268; 95% CI: 1.108-1.451; P < 0.001), while a negative association was observed with UC (OR = 0.839; 95% CI: 0.710-0.993; P = 0.041). These findings were supported by another set of RA data. Additionally, an SNP rs2071475 was identified to play an important role in CD and UC. CONCLUSION This study revealed a potential increased susceptibility to CD and a decreased susceptibility to UC in the East Asian population with RA. Furthermore, a key SNP rs2071475 was discovered along with its opposite effects in CD and UC. These findings provide new evidence for research on the corresponding molecular mechanisms and offer insights for clinical management of RA-associated IBD.
Collapse
Affiliation(s)
- Bo Wang
- Department of Geriatric Digestive Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 West 5th Road, Xi'an, 710004, Shaanxi, China
| | - Yongqiang Xiong
- Department of Geriatric Digestive Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 West 5th Road, Xi'an, 710004, Shaanxi, China
| | - Ren Li
- Department of Geriatric Digestive Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 West 5th Road, Xi'an, 710004, Shaanxi, China
| | - Shu Zhang
- Department of Geriatric Digestive Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, 157 West 5th Road, Xi'an, 710004, Shaanxi, China.
- Experimental Teaching Center for Clinical Skills, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
| |
Collapse
|
24
|
Wang Y, Qi H, Wang T, Zhang W, Shi X, Zhan Q, Li Q, Zhong M. STAT3 and STAT6 polymorphisms predict the severity of adverse reactions in Chinese NSCLC patients receiving EGFR-TKIs therapy. J Chemother 2024; 36:61-71. [PMID: 37151185 DOI: 10.1080/1120009x.2023.2203610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/12/2023] [Indexed: 05/09/2023]
Abstract
A total of 162 non-small cell lung cancer (NSCLC) patients were divided into discovery (N = 68) and validation (N = 94) groups. Nine Janus kinase/Signal transducer and activator of transcription (JAK/STAT) pathway-related single nucleotide polymorphisms were selected to explore the potential associations between genetic polymorphisms and adverse drug reactions (ADRs). The TT genotype of STAT6 rs324011 was significantly associated with severe ADRs in the recessive genetic model (TT vs. CC + CT, OR = 13.5, 95% CI = 2.12-86.09, p = 0.006 in the discovery group; OR = 8.41, 95% CI = 1.95-36.19, p = 0.004 in the validation group). The T allele was associated with a higher incidence of severe ADRs than was the C allele of rs324011 (OR = 3.67, 95% CI = 1.46-9.19, p = 0.006 in the discovery group; OR = 3.17, 95% CI = 1.44-6.99, p = 0.004 in the validation group). Patients with the CC genotype in STAT3 rs1053023 (and rs1053005) or the TT genotype of STAT6 rs324011 were likely to experience severe epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) related ADRs.
Collapse
Affiliation(s)
- Yan Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Huijie Qi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Tianxiao Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenxin Zhang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaojin Shi
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Qiong Zhan
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qunyi Li
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Mingkang Zhong
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
25
|
Zorina-Lichtenwalter K, Ase AR, Verma V, Parra AIM, Komarova S, Khadra A, Séguéla P, Diatchenko L. Characterization of Common Genetic Variants in P2RX7 and Their Contribution to Chronic Pain Conditions. J Pain 2024; 25:545-556. [PMID: 37742908 DOI: 10.1016/j.jpain.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/22/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
The adenosine triphosphate (ATP)-gated channel P2X7 is encoded by a gene enriched for common nonsynonymous variants. Many of these variants have functional cellular effects, and some have been implicated in chronic pain. In this study, we first systematically characterized all 17 common nonsynonymous variants using whole-cell patch clamp electrophysiology. Then, we analyzed these variants for statistical association with chronic pain phenotypes using both individual P2RX7 variants as predictors and cumulative allele counts of same-direction cellular effect in univariate models. Association and validation analyses were conducted in the Orofacial Pain: Prospective Evaluation and Risk Assessment (OPPERA) cohort (N = 3260) and in the Complex Persistent Pain Conditions (CPPC) cohort (N = 900), respectively. Our results showed an association between allele A of rs7958311 and an increased risk of chronic pelvic pain, with convergent evidence for contribution to fibromyalgia and irritable bowel syndrome, confirmed in a meta-analysis. This allelic variant produced a unique cellular phenotype: a gain-of-function in channel opening, and a loss-of-function in pore opening. A computational study using a 12-state Markov model of ATP binding to the P2X7 receptor suggested that this cellular phenotype arises from an increased ATP binding affinity and an increased open channel conductance combined with a loss of sensitization. Cumulative allele count analysis did not provide additional insights. In conclusion, our results go beyond reproducing association for rs7958311 with chronic pain and suggest that its unique combination of gain-of-function in channel and loss-of-function in pore activity may explain why it is likely the only common P2RX7 variant with contribution to chronic pain. PERSPECTIVE: This study characterizes all common P2RX7 variants using cellular assays and statistical association analyses with chronic pain, with Markov state modeling of the most robustly associated variant.
Collapse
Affiliation(s)
- Katerina Zorina-Lichtenwalter
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Alan Edwards Centre for Research on Pain, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Ariel R Ase
- Department of Neurology & Neurosurgery, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Montreal Neurological Institute/Hospital, Montreal, QC, Canada; Alan Edwards Centre for Research on Pain, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Vivek Verma
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Alan Edwards Centre for Research on Pain, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Arturo I M Parra
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Alan Edwards Centre for Research on Pain, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Svetlana Komarova
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| | - Anmar Khadra
- Department of Physiology, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Philippe Séguéla
- Department of Neurology & Neurosurgery, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Montreal Neurological Institute/Hospital, Montreal, QC, Canada; Alan Edwards Centre for Research on Pain, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Luda Diatchenko
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Alan Edwards Centre for Research on Pain, Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC, Canada
| |
Collapse
|
26
|
Muccee F, Ashraf NM, Razak S, Afsar T, Hussain N, Husain FM, Shafique H. Exploring the association of ESR1 and ESR2 gene SNPs with polycystic ovary syndrome in human females: a comprehensive association study. J Ovarian Res 2024; 17:27. [PMID: 38281964 PMCID: PMC10823698 DOI: 10.1186/s13048-023-01335-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/25/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Polycystic Ovary Syndrome (PCOS) affects a significant proportion of human females worldwide and is characterized by hormonal, metabolic, and reproductive dysfunctions, including infertility, irregular menstrual cycles, acanthosis nigricans, and hirsutism. Mutations in the estrogen receptor genes ESR1 and ESR2, involved in normal follicular development and ovulation, can contribute to development of the PCOS. The present study focuses on investigating the potential correlation between single nucleotide polymorphisms (SNPs) of ESR1 and ESR2 genes and the incidence of this syndrome. METHODS For this study, SNPs in ESR1 and ESR2 genes were retrieved from the ENSEMBL database and analyzed for their effect on mutated proteins using different bioinformatics tools including SIFT, PolyPhen, CADD, REVEL, MetaLR, I-Mutant, CELLO2GO, ProtParam, SOPMA, SWISS-MODEL and HDDOCK. RESULTS All the SNPs documented in the present study were deleterious. All the SNPs except rs1583384537, rs1450198518, and rs78255744 decreased protein stability. Two variants rs1463893698 and rs766843910 in the ESR2 gene altered the localization of mutated proteins i.e. in addition to the nucleus, proteins were also found in mitochondria and extracellular, respectively. SNPs rs104893956 in ESR1 and rs140630557, rs140630557, rs1596423459, rs766843910, rs1596405923, rs762454979 and rs1384121511 in ESR2 gene significantly changed the secondary structure of proteins (2D). SNPs that markedly changed 3D configuration included rs1554259481, rs188957694 and rs755667747 in ESR1 gene and rs1463893698, rs140630557, rs1596423459, rs766843910, rs1596405923, rs762454979 and rs1384121511 in ESR2 gene. Variants rs1467954450 (ESR1) and rs140630557 (ESR2) were identified to reduce the binding tendency of ESRα and β receptors with estradiol as reflected by the docking scores i.e. -164.97 and -173.23, respectively. CONCLUSION Due to the significant impact on the encoded proteins, these variants might be proposed as biomarkers to predict the likelihood of developing PCOS in the future and for diagnostic purposes.
Collapse
Affiliation(s)
- Fatima Muccee
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, 52254, Pakistan.
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of Punjab, Lahore, 52254, Pakistan
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain Campus, 64141, Al Ain, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi Campus, P. O. Box 112612, Abu Dhabi, United Arab Emirates
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Huma Shafique
- Institute of Cellular Medicine, Newcastle University Medical School, Newcastle University Newcastle Upon Tyne, Newcastle upon Tyne, UK
| |
Collapse
|
27
|
Fernández-Torres J, Zamudio-Cuevas Y, Martínez-Flores K, Franco-Cendejas R. Relationship between biofilm-forming microorganisms (BFM: Staphylococcus aureus and Pseudomonas aeruginosa) and DEFB1 gene variants on β-defensin levels in periprosthetic joint infection (PJI). Mol Biol Rep 2024; 51:237. [PMID: 38285273 DOI: 10.1007/s11033-023-09126-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND The purpose of this study was to investigate the relationship between biofilm-forming microorganisms (BFM) and DEFB1 gene variants on β-defensin levels in patients with periprosthetic joint infection (PJI) of Mexican origin. METHODS AND RESULTS One hundred and five clinical aspirates were obtained from patients with suspected PJI. After microbiologic culture, samples were classified as non-septic and septic; of the latter, only those positive for Staphylococcus aureus and Pseudomonas aeruginosa were selected. β-Defensin levels were quantified by ELISA, DNA was extracted from total leukocytes of the samples, and - 20G > A (rs11362) and - 44 C > G (rs1800972) variants were genotyped using TaqMan probes. Forty-one clinical aspirates were non-septic, 18 were positive for S. aureus and 18 were positive for P. aeruginosa. It was observed that β-defensin levels were higher in the P. aeruginosa group compared to S. aureus group (2339.0 pg/mL IQR = 1809.2 vs. 1821.3 pg/mL IQR = 1536.4) and non-septic group (2339.0 pg/mL IQR = 1809.2 vs. 1099.7 pg/mL IQR = 1744.5, P < 0.001). The CG genotype of the rs1800972 variant was associated with higher β-defensin levels compared to the CC genotype for both P. aeruginosa and S. aureus (1905.8 vs. 421.7 pg/mL, P = 0.004; and 1878.2 vs. 256.4 pg/mL, P = 0.006, respectively). CONCLUSIONS Our results show that β-defensin levels are significantly elevated in patients with BFM-associated PJI compared to those without infection. Furthermore, carriers of the CG genotype of the rs1800972 variant have an increased risk of PJI. Further research is needed to replicate these findings in a larger population.
Collapse
Affiliation(s)
- Javier Fernández-Torres
- Laboratorio de Líquido Sinovial, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389, Ciudad de México, México.
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de Mexico (UNAM), 04510, Ciudad de México, México.
| | - Yessica Zamudio-Cuevas
- Laboratorio de Líquido Sinovial, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389, Ciudad de México, México
| | - Karina Martínez-Flores
- Laboratorio de Líquido Sinovial, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389, Ciudad de México, México
| | - Rafael Franco-Cendejas
- División de Infectología, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389, Ciudad de México, México
- Subdirección de Investigación Biomédica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389, Ciudad de México, México
| |
Collapse
|
28
|
Qu YD, Jiang N, Li JX, Zhang W, Xia CL, Ou SJ, Yang Y, Ma YF, Qi Y, Xu CP. Chronic osteomyelitis risk is associated with NLRP3 gene rs10754558 polymorphism in a Chinese Han Population. BMC Med Genomics 2024; 17:38. [PMID: 38287380 PMCID: PMC10823619 DOI: 10.1186/s12920-024-01799-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/08/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) in the nucleotide-binding domain leucine-rich repeat protein-3 (NLRP3) gene are reported to be linked to many inflammatory disorders. However, uncertainty persists over the associations between these SNPs and susceptibilities to chronic osteomyelitis (COM). This study aimed to investigate potential relationships between NLRP3 gene SNPs and the risks of developing COM in a Chinese Han cohort. METHODS The four tag SNPs of the NLRP3 gene were genotyped in a total of 428 COM patients and 368 healthy controlsusing the SNapShot technique. The genotype distribution, mutant allele frequency, and the four genetic models (dominant, recessive, homozygous, and heterozygous) of the four SNPs were compared between the two groups. RESULTS A significant association was found between rs10754558 polymorphism and the probability of COM occurence by the heterozygous model (P = 0.037, odds ratio [OR] = 1.541, 95% confidence interval [CI] = 1.025-2.319), indicating that rs10754558 may be associated with a higher risk of developing COM.In addition, possible relationship was found between rs7525979 polymorphism and the risk of COM development by the outcomes of homozygous (P = 0.073, OR = 0.453, 95% CI = 0.187-1.097) and recessive (P = 0.093, OR = 0.478, 95% CI = 0.198-1.151) models, though no statistical differences were obtained. CONCLUSIONS Outcomes of the present study showed, for the first time, that rs10754558 polymorphism of the NLRP3 gene may increase the risk of COM development in this Chinese Han population, with genotype CG as a risk factor. Nonetheless, this conclusion requires verification from further studies with a larger sample size.
Collapse
Grants
- 81972083, 82172197 National Natural Science Foundation of China
- 81972083, 82172197 National Natural Science Foundation of China
- 2020A0505100039 Guangdong Provincial Science and Technology Project
- 2022A1515012385 Guangdong Basic and Applied Basic Research Foundation
- 202201020303, 202102080052, 202102010057, 201804010226 Science and Technology Planning Project of Guangzhou
- 202201020303, 202102080052, 202102010057, 201804010226 Science and Technology Planning Project of Guangzhou
- 3D-A2020004, 3D-A2020002, YQ2019-009, C2020019 Science Foundation of Guangdong Second Provincial General Hospital
- 3D-A2020004, 3D-A2020002, YQ2019-009, C2020019 Science Foundation of Guangdong Second Provincial General Hospital
Collapse
Affiliation(s)
- Yu-Dun Qu
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China
| | - Nan Jiang
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Jia-Xuan Li
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China
| | - Wei Zhang
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China
| | - Chang-Liang Xia
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China
| | - Shuan-Ji Ou
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China
| | - Yang Yang
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China
| | - Yun-Fei Ma
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Yong Qi
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China.
| | - Chang-Peng Xu
- Department of Orthopaedics, Guangdong Second Provincial General Hospital, 466 Xingang Road, Haizhu District, 510317, Guangzhou, China.
| |
Collapse
|
29
|
Li Y, Li J, Tang X, Xu J, Liu R, Jiang L, Tian J, Zhang Y, Wang D, Sun K, Xu B, Zhao W, Hui R, Gao R, Song L, Yuan J, Zhao X. Association of NPC1L1 and HMGCR gene polymorphisms with coronary artery calcification in patients with premature triple-vessel coronary disease. BMC Med Genomics 2024; 17:22. [PMID: 38233830 PMCID: PMC10795340 DOI: 10.1186/s12920-024-01802-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Coronary artery calcification (CAC) is a highly specific marker of atherosclerosis. Niemann-Pick C1-like 1 (NPC1L1) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) are the therapeutic targets of ezetimibe and statins, respectively, which are important for the progression of atherosclerosis. However, CAC's genetic susceptibility with above targets is still unknown. We aimed to investigate the association of NPC1L1 and HMGCR gene polymorphisms with CAC in patients with premature triple-vessel disease (PTVD). METHODS Four single nucleotide polymorphisms (SNPs) (rs11763759, rs4720470, rs2072183, rs2073547) of NPC1L1, and three SNPs (rs12916, rs2303151, rs4629571) of HMGCR were genotyped in 872 PTVD patients. According to the coronary angiography results, patients were divided into low-degree CAC group and high-degree CAC group. RESULTS A total of 872 PTVD patients (mean age, 47.71 ± 6.12; male, 72.8%) were finally included for analysis. Multivariate logistic regression analysis showed no significant association between the SNPs of NPC1L1 and HMGCR genes and high-degree CAC in the total population (P > 0.05). Subgroup analysis by gender revealed that the variant genotype (TT/CT) of rs4720470 on NPC1L1 gene was associated with increased risk for high-degree CAC in male patients only (OR = 1.505, 95% CI: 1.008-2.249, P = 0.046) in dominant model, but no significant association was found in female population, other SNPs of NPC1L1 and HMGCR genes (all P > 0.05). CONCLUSIONS We reported for the first time that the rs4720470 on NPC1L1 gene was associated with high-degree CAC in male patients with PTVD. In the future, whether therapies related to this target could reduce CAC and cardiovascular events deserves further investigation.
Collapse
Affiliation(s)
- Yulong Li
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Jiawen Li
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Xiaofang Tang
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Jingjing Xu
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Ru Liu
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Lin Jiang
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Jian Tian
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Yin Zhang
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Dong Wang
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Kai Sun
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Bo Xu
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Wei Zhao
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Rutai Hui
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Runlin Gao
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China
| | - Lei Song
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China.
| | - Jinqing Yuan
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China.
| | - Xueyan Zhao
- National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 167 Beilishi Road, Xicheng District, Beijing, 100037, China.
| |
Collapse
|
30
|
de Joode K, Heersche N, Basak EA, Bins S, van der Veldt AAM, van Schaik RHN, Mathijssen RHJ. Review - The impact of pharmacogenetics on the outcome of immune checkpoint inhibitors. Cancer Treat Rev 2024; 122:102662. [PMID: 38043396 DOI: 10.1016/j.ctrv.2023.102662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/05/2023]
Abstract
The development of immune checkpoint inhibitors (ICIs) has a tremendous effect on the treatment options for multiple types of cancer. Nonetheless, there is a large interpatient variability in response, survival, and the development of immune-related adverse events (irAEs). Pharmacogenetics is the general term for germline genetic variations, which may cause the observed interindividual differences in response or toxicity to treatment. These genetic variations can either be single-nucleotide polymorphisms (SNPs) or structural variants, such as gene deletions, amplifications or rearrangements. For ICIs, pharmacogenetic variation in the human leukocyte antigen molecules has also been studied with regard to treatment outcome. This review presents a summary of the literature regarding the pharmacogenetics of ICI treatment, discusses the most important known genetic variations and offers recommendations on the application of pharmacogenetics for ICI treatment.
Collapse
Affiliation(s)
- Karlijn de Joode
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Niels Heersche
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Clinical Chemistry, Erasmus MC, Erasmus University Hospital, Rotterdam, the Netherlands
| | - Edwin A Basak
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Sander Bins
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, Erasmus University Hospital, Rotterdam, the Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus MC, Erasmus University Hospital, Rotterdam, the Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
| |
Collapse
|
31
|
Lizárraga D, Gómez-Gil B, García-Gasca T, Ávalos-Soriano A, Casarini L, Salazar-Oroz A, García-Gasca A. Gestational diabetes mellitus: genetic factors, epigenetic alterations, and microbial composition. Acta Diabetol 2024; 61:1-17. [PMID: 37660305 DOI: 10.1007/s00592-023-02176-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Gestational diabetes mellitus (GDM) is a common metabolic disorder, usually diagnosed during the third trimester of pregnancy that usually disappears after delivery. In GDM, the excess of glucose, fatty acids, and amino acids results in foetuses large for gestational age. Hyperglycaemia and insulin resistance accelerate the metabolism, raising the oxygen demand, and creating chronic hypoxia and inflammation. Women who experienced GDM and their offspring are at risk of developing type-2 diabetes, obesity, and other metabolic or cardiovascular conditions later in life. Genetic factors may predispose the development of GDM; however, they do not account for all GDM cases; lifestyle and diet also play important roles in GDM development by modulating epigenetic signatures and the body's microbial composition; therefore, this is a condition with a complex, multifactorial aetiology. In this context, we revised published reports describing GDM-associated single-nucleotide polymorphisms (SNPs), DNA methylation and microRNA expression in different tissues (such as placenta, umbilical cord, adipose tissue, and peripheral blood), and microbial composition in the gut, oral cavity, and vagina from pregnant women with GDM, as well as the bacterial composition of the offspring. Altogether, these reports indicate that a number of SNPs are associated to GDM phenotypes and may predispose the development of the disease. However, extrinsic factors (lifestyle, nutrition) modulate, through epigenetic mechanisms, the risk of developing the disease, and some association exists between the microbial composition with GDM in an organ-specific manner. Genes, epigenetic signatures, and microbiota could be transferred to the offspring, increasing the possibility of developing chronic degenerative conditions through postnatal life.
Collapse
Affiliation(s)
- Dennise Lizárraga
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Bruno Gómez-Gil
- Laboratory of Microbial Genomics, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Teresa García-Gasca
- Laboratory of Molecular and Cellular Biology, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de las Ciencias s/n, 76230, Juriquilla, Querétaro, Mexico
| | - Anaguiven Ávalos-Soriano
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico
| | - Livio Casarini
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, via G. Campi 287, 41125, Modena, Italy
| | - Azucena Salazar-Oroz
- Maternal-Fetal Department, Instituto Vidalia, Hospital Sharp Mazatlán, Avenida Rafael Buelna y Dr. Jesús Kumate s/n, 82126, Mazatlán, Sinaloa, Mexico
| | - Alejandra García-Gasca
- Laboratory of Molecular and Cell Biology, Centro de Investigación en Alimentación y Desarrollo, Avenida Sábalo Cerritos s/n, 82112, Mazatlán, Sinaloa, Mexico.
| |
Collapse
|
32
|
Ebissy E, Darwish A, Hafez AA, Ateya A, El-Sayed A. Individual genomic loci, transcript level, and biochemical profile of immune and antioxidant markers associated with genetically identified bacterial mastitis in Shami goats in Egypt. Open Vet J 2024; 14:370-388. [PMID: 38633191 PMCID: PMC11018405 DOI: 10.5455/ovj.2024.v14.i1.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/15/2023] [Indexed: 04/19/2024] Open
Abstract
Background Mastitis in goats is unquestionably a grave concern, with far-reaching implications for both animal well-being and productivity, while also presenting a potential threat to public health. Aim The study aimed to compare culture methods and multiplex PCR (m-PCR) in the detection of the most three common mastitis-causing pathogens (Staphylococcus aureus, Escherichia coli, and Streptococcus spp.) and investigate the gene expression, single nucleotide polymorphisms (SNPs), serum concentrations of immunological and antioxidant indicators linked to mastitis in Shami goats. Methods One hundred Shami do (50 Shami goats with clinical mastitis and 50 normal goats taken as control group). The culture methods and m-PCR analysis were used to find the bacteria in the milk samples. Blood samples were obtained to assess some hemato-biochemical parameters, detect SNPs, and determine the expression of certain immunological and antioxidant indicators in the genes. Results The culture method detected the pathogens causing mastitis in 90% of the milk samples, but m-PCR detected them in 100% of the milk samples. SNPs linked to mastitis resistance/susceptibility in examined does were detected through DNA sequencing of immunological and antioxidant indicators. The magnitude of gene expression varied significantly between the resistant and mastitis-affected groups. Significant (P ˂ 0.05) elevations were noticed in WBCs count, mainly neutsrophils count, serum levels of BHB, NEFA, triglycerides, LDL-C, AST, ALT, ALP, creatinine, total protein, globulin, Ca, K, GPx, MDA, acute phase proteins, and cytokines in mastitis affected does as compared to control. While RBCs count, PCV%, lymphocytes count, serum concentration of glucose, cholesterol, HDL-C, albumin, Na, Cl, P, GSH, SOD, and catalase significantly (P ˂ 0.05) diminished in mastitis affected does compared to healthy ones. APPs and pro-inflammatory cytokines scored high sensitivities and NPVs but TNF-α and serum amyloid A (SAA) had the highest percentages of increase. Conclusion The study confirmed that m-PCR is the most sensitive method for bacteria identification (S. aureus, E. coli, and Strept. spp.) while SNPs in antioxidant and immunological genes may be important genetic indicators for mastitis risk or resistance in Shami does. To establish an effective management plan and forecast the most sensitive risk time for illness onset, gene expression profiles of the tested genes may also be employed as proxy biomarkers. TNF-α and SAA may be precious indicators for the detection of caprine mastitis.
Collapse
Affiliation(s)
- Eman Ebissy
- Department of Animal Health and Poultry, Animal and Poultry Production Division, Desert Research Center (DRC), Cairo, Egypt
| | - Asmaa Darwish
- Department of Animal Health and Poultry, Animal and Poultry Production Division, Desert Research Center (DRC), Cairo, Egypt
| | - Amani A. Hafez
- Department of Animal Health and Poultry, Animal and Poultry Production Division, Desert Research Center (DRC), Cairo, Egypt
| | - Ahmed Ateya
- Department of Development of Animal Wealth, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Ahmed El-Sayed
- Department of Animal Health and Poultry, Animal and Poultry Production Division, Desert Research Center (DRC), Cairo, Egypt
| |
Collapse
|
33
|
Kemp J, Ladwig PM, Snyder MR. Alpha-1-Antitrypsin (A1AT) Proteotyping by LC-MS/MS. Methods Mol Biol 2024; 2750:95-106. [PMID: 38108970 DOI: 10.1007/978-1-0716-3605-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The diagnosis of alpha-1-antitrypsin (A1AT) deficiency is established by quantitation of protein concentration in serum (immunoassay) followed by determination of specific allelic variants by phenotyping (isoelectric focusing (IEF) gel electrophoresis) and/or allele-specific genotyping. Various phenotyping and genotyping methodologies are available, and each has their own advantages and disadvantages. As an alternative, mass spectrometry is emerging as a powerful tool in the identification and quantitation of proteins and peptides. The method described here, referred to as proteotyping, is a proteomic method using trypsin digestion and tandem mass spectrometry that detects the most common deficiency alleles, S and Z, associated with A1AT deficiency.This qualitative mass spectrometry method is based on the principle that the S and Z mutations lead to amino acid changes which result in a change in the mass of the A1AT protein. When the A1AT protein is proteolytically digested, multiple peptides are generated, two of which include the sites of the S and Z mutations, respectively. Peptides generated from wild-type A1AT (M alleles) differ in sequence and mass from peptides generated from the S and Z alleles at these two specific locations. The mass difference allows for differentiation of S and Z peptides, representing the deficiency alleles, from non-S and non-Z peptides, representing the wild-type alleles (M). Interpretation of the peptide patterns in conjunction with A1AT quantitation by immunoassay allows for an accurate assessment for the presence of deficiency alleles in the majority of patients.
Collapse
Affiliation(s)
- Jennifer Kemp
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paula M Ladwig
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Melissa R Snyder
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
34
|
Lee SG, Eom SY, Lim JA, Choi BS, Kwon HJ, Hong YS, Kim YD, Kim H, Park JD. Association between urinary arsenic concentration and genetic polymorphisms in Korean adults. Toxicol Res 2024; 40:179-188. [PMID: 38223675 PMCID: PMC10786758 DOI: 10.1007/s43188-023-00216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/10/2023] [Accepted: 10/25/2023] [Indexed: 01/16/2024] Open
Abstract
Arsenic (As) is a human carcinogen widely distributed in the environment. This study evaluated the association between the urinary As concentration and single nucleotide polymorphisms (SNPs) in Korean adults to determine the genetic factors related to As concentration. The study included 496 participants for the genome-wide association study (GWAS) and 1483 participants for the candidate gene approach study. Participants were 19 years and older. The concentrations of total As (Tot As) and total As metabolites (Tmet As, the sum of inorganic As and their metabolites; arsenite, arsenate, monomethylarsonic, and dimethylarsinic acid) in the urine were analyzed. The GWAS identified four SNPs (rs1432523, rs3776006, rs11171747, and rs807573) associated with urinary Tot As and four SNPs (rs117605537, rs3776006, rs11171747, and rs148103384) significantly associated with urinary Tmet As concentration (P < 1 × 10-4). The candidate gene study identified two SNPs (PRDX2 rs10427027 and GLRX rs3822751) in genes related to the reduction reaction associated with urinary Tot As and Tmet As. This study suggests that genetic factors may play a role in regulating As metabolism in the human body, affecting both exposure levels and its potential health risks in the general Korean population, even at low exposure levels. Supplementary Information The online version contains supplementary material available at 10.1007/s43188-023-00216-x.
Collapse
Affiliation(s)
- Seul-Gi Lee
- Department of Preventive Medicine, College of Medicine, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974 Republic of Korea
| | - Sang-Yong Eom
- Department of Preventive Medicine, College of Medicine, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Ji-Ae Lim
- Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, 16890 Republic of Korea
| | - Byung-Sun Choi
- Department of Preventive Medicine, College of Medicine, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974 Republic of Korea
| | - Ho-Jang Kwon
- Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, 16890 Republic of Korea
| | - Young-Seoub Hong
- Department of Preventive Medicine, College of Medicine, Dong-A University, Busan, 49201 Republic of Korea
| | - Yong-Dae Kim
- Department of Preventive Medicine, College of Medicine, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Heon Kim
- Department of Preventive Medicine, College of Medicine, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Jung-Duck Park
- Department of Preventive Medicine, College of Medicine, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974 Republic of Korea
| |
Collapse
|
35
|
Saleem S, Imran Z, Samdani A, Khoso B, Zehra S, Azhar A. Mutations in PGRN gene associated with the risk of psoriasis in Pakistan: a case control study. BMC Med Genomics 2023; 16:335. [PMID: 38129828 PMCID: PMC10740244 DOI: 10.1186/s12920-023-01757-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Psoriasis is a chronic, autoimmune, papulosquamous skin disorder, characterized by the formation of drop-like papules and silvery-white plaques surrounded by reddened or inflamed skin, existing predominantly on the scalp, knees and elbows. The characteristic inflammation and hyperproliferation of keratinocytes in psoriasis is regulated by progranulin (PGRN), which suppresses the expression and release of inflammatory cytokines, such as TNF-α. METHODOLOGY In this study mutation analysis of the PGRN gene was performed by extracting the genomic DNA from blood samples of 171 diagnosed psoriasis patients and controls through standard salting-out method, followed by amplification and sequencing of the targeted region of exon 5-7 of PGRN gene. RESULTS Three single nucleotide polymorphisms, rs25646, rs850713 and a novel point mutation 805A/G were identified in the PGRN gene with significant association with the disease. The variant alleles of the polymorphisms were significantly distributed among cases and controls, and statistical analysis suggested that the mutant genotypes conferred a higher risk of psoriasis development and progression. Multi-SNP haplotype analysis indicated that the CAA (OR = 8.085, 95% CI = 5.16-12.66) and the CAG (OR = 3.204, 95% CI = 1.97-5.21) haplotypes were significantly associated with psoriasis pathogenesis. CONCLUSIONS These findings demonstrate that polymorphisms in PGRN might act as potential molecular targets for early diagnosis of psoriasis in susceptible individuals.
Collapse
Affiliation(s)
- Saima Saleem
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan.
| | - Zunaira Imran
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan
| | - Azam Samdani
- Department of Dermatology, National Medical Centre (NMC), Karachi, Pakistan
| | - Bahram Khoso
- Department of Dermatology, Jinnah Sindh Medical University (JSMU), Karachi, Pakistan
| | - Sitwat Zehra
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan
| | - Abid Azhar
- The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi, Karachi, Pakistan
| |
Collapse
|
36
|
Lozada DN, Sandhu KS, Bhatta M. Ridge regression and deep learning models for genome-wide selection of complex traits in New Mexican Chile peppers. BMC Genom Data 2023; 24:80. [PMID: 38110866 PMCID: PMC10726521 DOI: 10.1186/s12863-023-01179-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Genomewide prediction estimates the genomic breeding values of selection candidates which can be utilized for population improvement and cultivar development. Ridge regression and deep learning-based selection models were implemented for yield and agronomic traits of 204 chile pepper genotypes evaluated in multi-environment trials in New Mexico, USA. RESULTS Accuracy of prediction differed across different models under ten-fold cross-validations, where high prediction accuracy was observed for highly heritable traits such as plant height and plant width. No model was superior across traits using 14,922 SNP markers for genomewide selection. Bayesian ridge regression had the highest average accuracy for first pod date (0.77) and total yield per plant (0.33). Multilayer perceptron (MLP) was the most superior for flowering time (0.76) and plant height (0.73), whereas the genomic BLUP model had the highest accuracy for plant width (0.62). Using a subset of 7,690 SNP loci resulting from grouping markers based on linkage disequilibrium coefficients resulted in improved accuracy for first pod date, ten pod weight, and total yield per plant, even under a relatively small training population size for MLP and random forest models. Genomic and ridge regression BLUP models were sufficient for optimal prediction accuracies for small training population size. Combining phenotypic selection and genomewide selection resulted in improved selection response for yield-related traits, indicating that integrated approaches can result in improved gains achieved through selection. CONCLUSIONS Accuracy values for ridge regression and deep learning prediction models demonstrate the potential of implementing genomewide selection for genetic improvement in chile pepper breeding programs. Ultimately, a large training data is relevant for improved genomic selection accuracy for the deep learning models.
Collapse
Affiliation(s)
- Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
| | | | | |
Collapse
|
37
|
Lu C, Li S, Li Y, Zhang X, Chi J, Jiang Q, Ma Y, Shi X, Wang L, Li J. Associations between polymorphisms in the cannabinoid receptor 1 gene, cognitive impairments and tardive dyskinesia in a Chinese population with schizophrenia. Brain Res 2023; 1821:148579. [PMID: 37739333 DOI: 10.1016/j.brainres.2023.148579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/03/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
OBJECTIVE Tardive dyskinesia (TD) is a medically induced movement disorder that occurs as a result of long-term use of antipsychotic medications, commonly seen in patients with schizophrenia (SCZ). The study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) of the CNR1 gene, TD and cognitive impairments in a Chinese population with SCZ. METHODS A total of 216 SCZ patients were recruited. The participants were divided into TD and without TD (WTD) groups using the Schooler-Kane International Diagnostic Criteria. The severity of TD was assessed using the Abnormal Involuntary Movement Scale (AIMS). Cognitive function was assessed using the Repeatable Battery for Assessment of Neuropsychological Status (RBANS) scale. Hardy-Weinberg equilibrium tests, chained disequilibrium analyses and haplotype analyses were performed using SHE-sis software. To explore the main effects of TD diagnosis, genotype and cognitive function, as well as interaction effects, analysis of covariance (ANCOVA) was employed. RESULTS The prevalence of TD was approximately 27.3%. Significant differences were observed in the rs806368 CT genotype and rs806370 TC genotype within the hypercongenic pattern between the male TD and WTD groups (OR = 2.508, 95% CI: 1.055-5.961, p = 0.037; OR = 2.552, 95% CI: 1.073-6.069, p = 0.034). Among TD patients, those carrying the rs806368 CC genotype exhibited higher limb trunk scores (p < 0.05). Moreover, there was a statistically significant difference in visuospatial/construction between the TD and WTD groups (p = 0.04), and a borderline significant difference in visuospatial/construction when considering the interaction between TD diagnosis and genotype at the rs806368 locus (p = 0.05). CONCLUSION CNR1 rs806368 and rs806370 polymorphisms may play a role in TD susceptibility. Additionally, CNR1 gene polymorphisms were associated with the severity of involuntary movements and cognitive impairments in TD patients.
Collapse
Affiliation(s)
- Chenghao Lu
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Shen Li
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Yanzhe Li
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Xiaofei Zhang
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Jinghui Chi
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Qiaona Jiang
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Yanyan Ma
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Xiaomei Shi
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China
| | - Lili Wang
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China.
| | - Jie Li
- Tianjin Mental Health Institute, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300222, China.
| |
Collapse
|
38
|
Larsson SC, Butterworth AS, Burgess S. Mendelian randomization for cardiovascular diseases: principles and applications. Eur Heart J 2023; 44:4913-4924. [PMID: 37935836 PMCID: PMC10719501 DOI: 10.1093/eurheartj/ehad736] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/13/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
Large-scale genome-wide association studies conducted over the last decade have uncovered numerous genetic variants associated with cardiometabolic traits and risk factors. These discoveries have enabled the Mendelian randomization (MR) design, which uses genetic variation as a natural experiment to improve causal inferences from observational data. By analogy with the random assignment of treatment in randomized controlled trials, the random segregation of genetic alleles when DNA is transmitted from parents to offspring at gamete formation is expected to reduce confounding in genetic associations. Mendelian randomization analyses make a set of assumptions that must hold for valid results. Provided that the assumptions are well justified for the genetic variants that are employed as instrumental variables, MR studies can inform on whether a putative risk factor likely has a causal effect on the disease or not. Mendelian randomization has been increasingly applied over recent years to predict the efficacy and safety of existing and novel drugs targeting cardiovascular risk factors and to explore the repurposing potential of available drugs. This review article describes the principles of the MR design and some applications in cardiovascular epidemiology.
Collapse
Affiliation(s)
- Susanna C Larsson
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
| | - Stephen Burgess
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Papworth Road, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| |
Collapse
|
39
|
Matkarimov BT, Saparbaev MK. Chargaff's second parity rule lies at the origin of additive genetic interactions in quantitative traits to make omnigenic selection possible. PeerJ 2023; 11:e16671. [PMID: 38107580 PMCID: PMC10725672 DOI: 10.7717/peerj.16671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023] Open
Abstract
Background Francis Crick's central dogma provides a residue-by-residue mechanistic explanation of the flow of genetic information in living systems. However, this principle may not be sufficient for explaining how random mutations cause continuous variation of quantitative highly polygenic complex traits. Chargaff's second parity rule (CSPR), also referred to as intrastrand DNA symmetry, defined as near-exact equalities G ≈ C and A ≈ T within a single DNA strand, is a statistical property of cellular genomes. The phenomenon of intrastrand DNA symmetry was discovered more than 50 years ago; at present, it remains unclear what its biological role is, what the mechanisms are that force cellular genomes to comply strictly with CSPR, and why genomes of certain noncellular organisms have broken intrastrand DNA symmetry. The present work is aimed at studying a possible link between intrastrand DNA symmetry and the origin of genetic interactions in quantitative traits. Methods Computational analysis of single-nucleotide polymorphisms in human and mouse populations and of nucleotide composition biases at different codon positions in bacterial and human proteomes. Results The analysis of mutation spectra inferred from single-nucleotide polymorphisms observed in murine and human populations revealed near-exact equalities of numbers of reverse complementary mutations, indicating that random genetic variations obey CSPR. Furthermore, nucleotide compositions of coding sequences proved to be statistically interwoven via CSPR because pyrimidine bias at the 3rd codon position compensates purine bias at the 1st and 2nd positions. Conclusions According to Fisher's infinitesimal model, we propose that accumulation of reverse complementary mutations results in a continuous phenotypic variation due to small additive effects of statistically interwoven genetic variations. Therefore, additive genetic interactions can be inferred as a statistical entanglement of nucleotide compositions of separate genetic loci. CSPR challenges the neutral theory of molecular evolution-because all random mutations participate in variation of a trait-and provides an alternative solution to Haldane's dilemma by making a gene function diffuse. We propose that CSPR is symmetry of Fisher's infinitesimal model and that genetic information can be transferred in an implicit contactless manner.
Collapse
Affiliation(s)
- Bakhyt T. Matkarimov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- L.N.Gumilev Eurasian National University, Astana, Kazakhstan
| | - Murat K. Saparbaev
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| |
Collapse
|
40
|
Hamza H, Villa S, Torre S, Marchesini A, Benabderrahim MA, Rejili M, Sebastiani F. Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships. BMC Genomics 2023; 24:772. [PMID: 38093186 PMCID: PMC10720229 DOI: 10.1186/s12864-023-09872-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and has great traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value. However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencing has made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore the genetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail. RESULTS Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targeted bioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variant annotation and investigate patterns of evolutionary relationship. Our results revealed the existence of unique haplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs on genes functions was predicted in silico. CONCLUSIONS The results of this study have important implications, in the light of ongoing environmental changes, for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculture threatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvement programs of the date palm through selective cross-breeding.
Collapse
Affiliation(s)
- Hammadi Hamza
- Arid and Oases Cropping Laboratory, Arid Regions Institute, Route du Djorf, Medenine, 4119, Tunisia.
| | - Sara Villa
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy
| | - Alexis Marchesini
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy
- Research Institute on Terrestrial Ecosystems (IRET), National Research Council of Italy (CNR), via Marconi 2, Porano, Terni, 05010, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy
| | | | - Mokhtar Rejili
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources (BVBAA) - Faculty of Sciences of Gabes, University of Gabes, Erriadh, Gabes, 6072, Tunisia
- Department of Biology, College of Sciences, Al Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), via Madonna del Piano 10, Sesto Fiorentino, Florence, 50019, Italy.
| |
Collapse
|
41
|
Rasyid N, Soedarman S. Genes polymorphism as risk factor of recurrent urolithiasis: a systematic review and meta-analysis. BMC Nephrol 2023; 24:363. [PMID: 38066480 PMCID: PMC10709856 DOI: 10.1186/s12882-023-03368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/15/2023] [Indexed: 12/18/2023] Open
Abstract
INTRODUCTION Urolithiasis is one of the most prevalent diseases worldwide. Its prevalence is rising, both in developing and developed countries. It is known that genetic factors play big roles in the development of urolithiasis. One of the suspected factors is gene polymorphism. This study aims to find an accurate estimate of the association between genetic polymorphism and the risk of recurrent urolithiasis. METHODS A systematic review and meta-analysis were performed on 12 studies from 3 databases that investigated gene polymorphism as an risk factor of urolithiasis. The review was done using Review Manager® version 5.3. RESULTS Insignificant heterogenicity was found in this study. Populations from Asia and the Middle East are more likely to experience recurrent urolithiasis. Additionally, variation in the VDR and urokinase genes, particularly in the Asian population, increases the risk of developing recurrent urolithiasis. CONCLUSIONS Gene polymorphisms have significant roles in the development of urolithiasis, especially in the Middle Eastern region.
Collapse
Affiliation(s)
- Nur Rasyid
- Department of Urology, Faculty of Medicine, Cipto Mangunkusumo Hospital, University, Jakarta Pusat, Indonesia.
| | - Soefiannagoya Soedarman
- Department of Urology, Faculty of Medicine, Cipto Mangunkusumo Hospital, University, Jakarta Pusat, Indonesia
| |
Collapse
|
42
|
Huang YH, Chen YC, Ho WM, Lee RG, Chung RH, Liu YL, Chang PY, Chang SC, Wang CW, Chung WH, Tsai SJ, Kuo PH, Lee YS, Hsiao CC. Classifying Alzheimer's disease and normal subjects using machine learning techniques and genetic-environmental features. J Formos Med Assoc 2023:S0929-6646(23)00439-4. [PMID: 38044212 DOI: 10.1016/j.jfma.2023.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/24/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is complicated by multiple environmental and polygenetic factors. The accuracy of artificial neural networks (ANNs) incorporating the common factors for identifying AD has not been evaluated. METHODS A total of 184 probable AD patients and 3773 healthy individuals aged 65 and over were enrolled. AD-related genes (51 SNPs) and 8 environmental factors were selected as features for multilayer ANN modeling. Random Forest (RF) and Support Vector Machine with RBF kernel (SVM) were also employed for comparison. Model results were verified using traditional statistics. RESULTS The ANN achieved high accuracy (0.98), sensitivity (0.95), and specificity (0.96) in the intrinsic test for AD classification. Excluding age and genetic data still yielded favorable results (accuracy: 0.97, sensitivity: 0.94, specificity: 0.96). The assigned weights to ANN features highlighted the importance of mental evaluation, years of education, and specific genetic variations (CASS4 rs7274581, PICALM rs3851179, and TOMM40 rs2075650) for AD classification. Receiver operating characteristic analysis revealed AUC values of 0.99 (intrinsic test), 0.60 (TWB-GWA), and 0.72 (CG-WGS), with slightly lower AUC values (0.96, 0.80, 0.52) when excluding age in ANN. The performance of the ANN model in AD classification was comparable to RF, SVM (linear kernel), and SVM (RBF kernel). CONCLUSIONS The ANN model demonstrated good sensitivity, specificity, and accuracy in AD classification. The top-weighted SNPs for AD prediction were CASS4 rs7274581, PICALM rs3851179, and TOMM40 rs2075650. The ANN model performed similarly to RF and SVM, indicating its capability to handle the complexity of AD as a disease entity.
Collapse
Affiliation(s)
- Yu-Hua Huang
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Yi-Chun Chen
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Wei-Min Ho
- Department of Neurology, Chang Gung Memorial Hospital Linkou Medical Center and College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Ren-Guey Lee
- Department of Electronics Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Chaung-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei and Keelung, Taiwan; Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei and Keelung, Taiwan; Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan; Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan; Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
| | - Chun-Chieh Hsiao
- Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan; Department of Computer Information and Network Engineering, Lunghwa University of Science and Technology, Taoyuan, Taiwan.
| |
Collapse
|
43
|
Yang L, Xu Y, Zhou P, Wan G. The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia. Exp Eye Res 2023; 237:109694. [PMID: 37890754 DOI: 10.1016/j.exer.2023.109694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/11/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
The aim of this study was to explore the association between SNTB1 and ZFHX1B polymorphisms and high myopia (HM) in a Northern Han Chinese population. This case-control study included 457 HM and 860 healthy subjects from the Northern Han Chinese population. Four single nucleotide polymorphisms (SNPs) (rs7839488, rs4395927, rs4455882, and rs6469937) in SNTB1 and one SNP in ZFHX1B (rs13382811)were selected based on two previous genome-wide association study (GWAS) studies. The allele and genotype distributions of SNPs in SNTB1 and ZFHX1B were compared between the two groups using the chi-square test. The allele results were adjusted for age and sex using Plink software (Plink 1.9). Pairwise linkage disequilibrium (LD) and haplotype analyses were performed using SHEsis software. For HM subjects, the mean age was 44.80 ± 17.11 years, and for the control subjects, it was 44.41 ± 14.26 years. For rs7839488 of the SNTB1 gene, the A allele is a risk allele and the G allele is a wild allele. The A allele had no statistical significance with the HM cases and controls (OR = 0.90, 95% CI = 0.74-1.09, aP = 0.273, Pc = NS). There was a LD in SNTB1 (rs7839488, rs4395927, rs4455882, and rs6469937). The G-C-A-G haplotype frequency was higher in HM subjects than that of the controls (OR = 1.31, 95% CI = 1.07-1.60, P = 0.008). Meanwhile, the A-T-G-A haplotype frequency was slightly lower in the HM group (OR = 0.81, 95% CI = 0.66-0.99, P = 0.048). In the ZFHX1B gene, the frequency of the minor T allele of rs13382811 was significant higher in the HM group than in the control group (OR = 1.34, 95% CI = 1.11-1.61, aP = 0.001, Pc = 0.009). Furthermore, compared to the CC genotype, there were significant differences in the CT genotype (OR = 1.57, 95% CI = 1.23-2.00, aP < 0.001, Pc = 0.002). In conclusion, G-C-A-G is a risk haplotype from the SNTB1 gene in high myopia patients. The minor T-allele of ZFHX1B rs13382811 is a risk factor for high myopia. SNTB1 and ZFHX1B are both risk genes associated with increased susceptibility to high myopia in the Northern Han Chinese population.
Collapse
Affiliation(s)
- Lin Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Youmei Xu
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Pengyi Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Guangming Wan
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China.
| |
Collapse
|
44
|
Yin Y, Tong L, Wan Z, Sui Y, Li F, Huang Q, Zhao X. CYP4B1 polymorphisms and the risk of breast cancer in Chinese women: a case-control study. BMC Cancer 2023; 23:1177. [PMID: 38041008 PMCID: PMC10693087 DOI: 10.1186/s12885-023-11477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/03/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is one of the malignant diseases threatening the life and health of women worldwide. The CYP4B1 gene was abnormally expressed in BC and was associated with the prognosis of BC patients. This study aimed to explore the relationship between CYP4B1 single nucleotide polymorphisms (SNPs) and BC risk in Chinese women. METHODS A case-control study of 1,143 women (571 patients and 572 healthy individuals) was conducted. Rs2297813 G/T, rs12142787 G/A, and rs3766197 C/T in CYP4B1 were selected and genotyped by MassARRAY system. The relationships between these SNPs and the risk of BC were assessed by logistic regression analysis. In addition, multi-factor dimensionality reduction (MDR) was used to analyze SNP-SNP interactions. RESULTS CYP4B1 rs2297813 had a risk-increasing effect on BC in women with body mass index (BMI) ≤ 24 kg/m2 (OR = 1.72, p = 0.026). CYP4B1 rs12142787 was associated with an increased BC risk in smokers (AA: OR = 1.32, p = 0.045). Among non-drinkers, rs2297813 (OR = 1.69, p = 0.009) and rs12142787 (OR = 1.51, p = 0.020) were related to an increased incidence of BC. CYP4B1 rs3766197 (OR = 1.61p = 0.031) was associated with a higher risk of advanced stages (III/IV stage) of BC. Besides, the contributions of CYP4B1 rs2297813 (OR = 1.55, p = 0.021) and rs12142787 (OR = 1.53, p = 0.033) to BC risk might be associated with more than one birth in patients with BC. The three-locus model consisting of rs2297813, rs12142787, and rs3766197 was regarded as the best predictive model for BC risk. CONCLUSION CYP4B1 SNPs were associated with BC risk in Chinese women, especially in patients with BMI ≤ 24 kg/m2, smokers, non-drinkers, patients in advanced stages (III/IV stage), and patients who reproduced once. These findings shed light on the relationship between CYP4B1 SNPs and BC risk in Chinese women.
Collapse
Affiliation(s)
- Yanhai Yin
- Department of Internal Medicine Oncology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, No.76, Yanta West Road, Xi'an City, 710061, Shaanxi Province, China
- Department of Nuclear Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570208, China
| | - Liangqian Tong
- Department of Nuclear Medicine, Central South University Xiangya School Affiliated Haikou Hospital, Haikou, Hainan, 570208, China
| | - Zhenling Wan
- Department of Pathology, Hainan Women and Children Medical Center, Haikou, Hainan, 570208, China
| | - Yanfang Sui
- Department of Rehabilitation Medicine, Central South University Xiangya School Affiliated Haikou Hospital, Haikou, Hainan, 570208, China
| | - Fen Li
- Department of Nuclear Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570208, China
| | - Qian Huang
- Department of Nuclear Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570208, China
| | - Xinhan Zhao
- Department of Internal Medicine Oncology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, No.76, Yanta West Road, Xi'an City, 710061, Shaanxi Province, China.
| |
Collapse
|
45
|
Rabadán-Chávez G, Díaz de la Garza RI, Jacobo-Velázquez DA. White adipose tissue: Distribution, molecular insights of impaired expandability, and its implication in fatty liver disease. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166853. [PMID: 37611674 DOI: 10.1016/j.bbadis.2023.166853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
We are far behind the 2025 World Health Organization (WHO) goal of a zero increase in obesity. Close to 360 million people in Latin America and the Caribbean are overweight, with the highest rates observed in the Bahamas, Mexico, and Chile. To achieve relevant progress against the obesity epidemic, scientific research is essential to establish uniform practices in the study of obesity pathophysiology (using pre-clinical and clinical models) that ensure accuracy, reproducibility, and transcendent outcomes. The present review focuses on relevant aspects of white adipose tissue (WAT) expansion, underlying mechanisms of inefficient expandability, and its repercussion in ectopic lipid accumulation in the liver during nutritional abundance. In addition, we highlight the potential role of disrupted circadian rhythm in WAT metabolism. Since genetic factors also play a key role in determining an individual's predisposition to weight gain, we describe the most relevant genes associated with obesity in the Mexican population, underlining that most of them are related to appetite control.
Collapse
Affiliation(s)
- Griselda Rabadán-Chávez
- Tecnologico de Monterrey, Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, NL, Mexico
| | - Rocío I Díaz de la Garza
- Tecnologico de Monterrey, Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, NL, Mexico; Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Campus Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, NL, Mexico.
| | - Daniel A Jacobo-Velázquez
- Tecnologico de Monterrey, Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, NL, Mexico; Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Campus Guadalajara, Av. General Ramon Corona 2514, C.P. 45201 Zapopan, Jalisco, Mexico.
| |
Collapse
|
46
|
Amin M, Gragnoli C. The prolactin receptor gene (PRLR) is linked and associated with the risk of polycystic ovarian syndrome. J Ovarian Res 2023; 16:222. [PMID: 37993904 PMCID: PMC10664635 DOI: 10.1186/s13048-023-01280-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 09/12/2023] [Indexed: 11/24/2023] Open
Abstract
The prolactin receptor gene (PRLR) may contribute to polycystic ovarian syndrome (PCOS) since it plays important roles in physiological ovarian functions. PRLR-knockout mice have irregular cycles and subfertility and variants in or around the PRLR gene were associated in humans with female testosterone levels and recurrent miscarriage. We tested 40 variants in the PRLR gene in 212 Italian families phenotyped by type 2 diabetes (T2D) and PCOS and found two intronic PRLR-variants (rs13436213 and rs1604428) significantly linked to and/or associated with the risk of PCOS. This is the first study to report PRLR as a novel risk gene in PCOS. Functional studies are needed to confirm these results.
Collapse
Affiliation(s)
- Mutaz Amin
- INSERM, US14-Orphanet, Paris, 75014, France
| | - Claudia Gragnoli
- Division of Endocrinology, Department of Medicine, Creighton University School of Medicine, Omaha, NE, 68124, USA.
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA.
- Molecular Biology Laboratory, Bios Biotech Multi-Diagnostic Health Center, Rome, 00197, Italy.
| |
Collapse
|
47
|
Soler-Blasco R, Harari F, Riutort-Mayol G, Murcia M, Lozano M, Irizar A, Marina LS, Zubero MB, Fernández-Jimenez N, Braeuer S, Ballester F, Llop S. Influence of genetic polymorphisms on arsenic methylation efficiency during pregnancy: Evidence from a Spanish birth cohort. Sci Total Environ 2023; 900:165740. [PMID: 37495132 DOI: 10.1016/j.scitotenv.2023.165740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Inorganic arsenic (iAs) is a widespread toxic metalloid. It is well-known that iAs metabolism and its toxicity are mediated by polymorphisms in AS3MT and other genes. However, studies during pregnancy are scarce. We aimed to examine the role of genetic polymorphisms in AS3MT, GSTO2, N6AMT1, MTHFR, MTR, FTCD, CBS, and FOLH1 in iAs methylation efficiency during pregnancy. METHODS The study included 541 pregnant participants from the INMA (Environment and Childhood) Spanish cohort. Using high-performance liquid chromatography coupled to inductively coupled plasma-tandem mass, we measured arsenic (iAs and the metabolites monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA)) in urine samples collected during the first trimester. iAs methylation efficiency was determined based on relative concentrations of the As metabolites in urine (%MMA, %DMA, and %iAs). Thirty-two single nucleotide polymorphisms (SNPs) in nine genes were determined in maternal DNA; AS3MT haplotypes were inferred. We assessed the association between genotypes/haplotypes and maternal As methylation efficiency using multivariate linear regression models. RESULTS The median %MMA and %DMA were 5.3 %, and 89 %, respectively. Ancestral alleles of AS3MT SNPs (rs3740393, rs3740390, rs11191453, and rs11191454) were significantly associated with higher %MMA, %iAs, and lower %DMA. Pregnant participants with zero copies of the GGCTTCAC AS3MT haplotype presented a higher %MMA. Statistically significant associations were also found for the FOLH1 SNP rs202676 (β 0.89 95%CI: 0.24, 1.55 for carriers of the G allele vs. the A allele). CONCLUSIONS Our study shows that ancestral alleles in AS3MT polymorphisms were associated with lower As methylation efficiency in early pregnancy and suggests that FOLH1 also plays a role in As methylation efficiency. These results support the hypothesis that As metabolism is multigenic, being a key element for identifying susceptible populations.
Collapse
Affiliation(s)
- Raquel Soler-Blasco
- Department of Nursing, Universitat de València, Valencia, Spain; Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Florencia Harari
- Occupational and Environmental Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Gabriel Riutort-Mayol
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, Valencia, Spain
| | - Mario Murcia
- Health Policy Planning and Evaluation Service, Conselleria de Sanitat Universal i Salut Pública, Generalitat Valenciana, Valencia, Spain
| | - Manuel Lozano
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain; Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department, Universitat de València, Valencia, Spain
| | - Amaia Irizar
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; Biodonostia Health Research Institute, San Sebastian, Spain; Departament of Preventive Medicine and Public Health of the University of the Basque Country, UPV/EHU, Bizkaia, Spain
| | - Loreto Santa Marina
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain; Biodonostia Health Research Institute, San Sebastian, Spain; Public Health Division of Gipuzkoa, Basque Government, San Sebastian, Spain
| | - Miren Begoña Zubero
- Departament of Preventive Medicine and Public Health of the University of the Basque Country, UPV/EHU, Bizkaia, Spain
| | - Nora Fernández-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Biocruces-Bizkaia Health Research Institute, University of the Basque Country (UPV/EHU), Bizkaia, Spain
| | - Simone Braeuer
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Ferran Ballester
- Department of Nursing, Universitat de València, Valencia, Spain; Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Sabrina Llop
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| |
Collapse
|
48
|
Yin Y, Zhang Y, Zhang X, Zhang Q, Wang J, Yang T, Liang C, Li W, Liu J, Ma X, Duan J, Shi W, Tian Y. Association of MMP3, MMP14, and MMP25 gene polymorphisms with cerebral stroke risk: a case-control study. BMC Med Genomics 2023; 16:297. [PMID: 37986083 PMCID: PMC10659043 DOI: 10.1186/s12920-023-01734-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Cerebral stroke (CS) is the leading cause of death in China, and a complex disease caused by both alterable risk factors and genetic factors. This study intended to investigate the association of MMP3, MMP14, and MMP25 single nucleotide polymorphisms (SNPs) with CS risk in a Chinese Han population. METHODS A total of 1,348 Han Chinese were recruited in this case-control study. Four candidate loci including rs520540 A/G and rs679620 T/C of MMP3, rs2236302 G/C of MMP14, and rs10431961 T/C of MMP25 were successfully screened. The correlation between the four SNPs and CS risk was assessed by logistic regression analysis. The results were analyzed by false-positive report probability (FPRP) for chance or significance. The interactions between four SNPs associated with CS risk were assessed by multifactor dimensionality reduction (MDR). RESULTS rs520540 A/G and rs679620 C/T SNP in MMP3 were associated with risk of CS in allele, codominant, dominant and log-additive models. Ischemic stroke risk were significantly lower in carriers with rs520540-A allele and rs679620-T allele than those with G/G or C/C genotypes. However, rs520540-A allele and rs679620-T allele were associated with higher risk of hemorrhagic stroke. Stratified analysis showed that these two SNPs were associated with reduced risk of CS in aged < 55 years, non-smoking and non-drinking participants, and rs679620 SNP also reduced CS risk in male participants. The levels of uric acid, high-density lipoprotein cholesterol, and eosinophil were different among patients with different genotypes of rs520540 and rs679620. No statistically significant association was found between MMP14 rs2236302 G/C or MMP25 rs10431961 T/C with CS even after stratification by stroke subtypes, age, gender as well as smoking and drinking conditions in all the genetic models. CONCLUSION MMP3 rs520540 A/G and rs679620 C/T polymorphisms were associated with CS risk in the Chinese Han population, which provides useful information for the prevention and diagnosis of CS.
Collapse
Affiliation(s)
- Yanling Yin
- Department of Neurology, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Yu Zhang
- The College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Xiaobo Zhang
- The College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Qi Zhang
- The College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiachen Wang
- The College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Tian Yang
- Clinical Medical Research Center, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Chen Liang
- Clinical Medical Research Center, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Wu Li
- Clinical Medical Research Center, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Jie Liu
- Clinical Medical Research Center, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Xiaojuan Ma
- Clinical Medical Research Center, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Jinwei Duan
- Clinical Medical Research Center, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Wenzhen Shi
- Clinical Medical Research Center, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China
| | - Ye Tian
- Department of Neurology, Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, 710018, China.
| |
Collapse
|
49
|
Fu L, Lei C, Chen Y, Xu X, Wu B, Dong L, Ye X, Zheng L, Gong D. Association of the rs3917647 polymorphism of the SELP gene with malnutrition in gastric cancer. Support Care Cancer 2023; 31:708. [PMID: 37978991 DOI: 10.1007/s00520-023-08161-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Malnutrition and cachexia are common syndromes in patients with gastric cancer (GC) and are associated with poor quality of life and poor disease prognosis. However, there is still a lack of molecular factors that can predict malnutrition or cachexia in cancer. Studies have shown that among the potential contributors to the development of cancer cachexia, the level of the inflammatory response to P-selectin is regulated by single nucleotide polymorphisms (SNPs) located in the promoter region of the SELP gene. The aim of this study was to evaluate the association between the single nucleotide polymorphism (SNP)-2028 A/G of the SELP gene and malnutrition in patients receiving chemotherapy for gastric cancer (GC). METHODS The study group consisted of 220 GC patients treated with chemotherapy at Jinhua Municipal Central Hospital. DNA was extracted from peripheral leukocytes of whole blood samples using an animal DNA extraction kit. DNA was amplified using a 1.1 × T3 Super PCR mix, and loci corresponding to the peaks were genotyped using SNP1 software. RESULTS Patients carrying the A allele had a reduced risk of developing malnutrition compared to patients with the GG genotype (P < 0.001; OR = 3.411; 95% CI = 1.785-6.516). In addition, multivariate analysis indicated that the AA genotype significantly (more than 16-fold) reduced the risk of developing malnutrition (P < 0.001; OR = 0.062; 95% CI = 0.015-0.255). CONCLUSION SELP -2028A/G SNP may be a useful marker for assessing the risk of malnutrition in GC patients.
Collapse
Affiliation(s)
- Liang Fu
- Department of Nursing, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Changzhen Lei
- Department of Gastrointestinal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Yingxun Chen
- Department of Nursing, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Xiaoqian Xu
- Department of Nursing, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Bei Wu
- Department of Nursing, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Liping Dong
- Department of Nursing, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Xianghong Ye
- Department of Nursing, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Lushan Zheng
- Department of Nursing, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China.
| | - Daojun Gong
- Department of Gastrointestinal Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China.
| |
Collapse
|
50
|
Aruna P, Patil SS, Muthu MS, Vettriselvi V, Arockiam S, Kirubakaran R, Sivakumar N. Association between polymorphisms of immune response genes and early childhood caries - systematic review, gene-based, gene cluster, and meta-analysis. J Genet Eng Biotechnol 2023; 21:124. [PMID: 37971556 PMCID: PMC10654314 DOI: 10.1186/s43141-023-00566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Early childhood caries is a significant public health concern affecting about 600 million children globally. The etiology of early childhood caries can be explained as an interplay between genetic and environmental factors. Single nucleotide polymorphisms are the most common variations in the human genome. Genetic variations of immune response genes can modify the defense response of the host, and alter the susceptibility to bacterial colonization of the oral cavity and early childhood caries. The aim of this systematic review is to identify genetic variants of immune response genes associated with early childhood caries. RESULTS A total of 7124 articles were identified by conducting an elaborate search across various electronic databases and genome-wide association studies databases. Subsequent to exclusion at various stages, fifteen articles qualified to be included into the present review. Risk of bias assessment was done with the Q-genie tool. Quantitative synthesis revealed that the odds ratio for TT and CC genotypes of rs11362 was 1.07 (0.67-1.71) and 1.16 (0.84-1.60), respectively. Gene-based analysis revealed a statistically significant association between variants of tumor necrosis factor-alpha gene and T-cell receptor alpha variable 4 locus with early childhood caries. Gene clustering showed the presence of three functional clusters. To comprehend the protein-protein interaction, the bioinformatic tool of "Search Tools for the Retrieval of Interacting Genes and Proteins" was used. Among the biological processes and the reactome pathways, complement activation through the lectin pathway showed the highest strength of association with early childhood caries. To understand the interaction and functionality of the genes, "gene function prediction using Multiple Association Network Integration Algorithm" was used, which revealed that the genes were linked by physical interaction (39.34%) and through co-expression (34.88%). CONCLUSIONS Genotype TT of rs7217186 of arachidonate 15-lipoxygenase gene was a risk factor for early childhood caries. Multiple genetic variants of T-cell receptor alpha variable 4 locus and tumor necrosis factor-alpha gene were associated with increased susceptibility to early childhood caries. Polymorphisms of genes regulating the lectin pathway of complement activation can modify the susceptibility to early childhood caries.
Collapse
Affiliation(s)
- P Aruna
- Centre for Early Childhood Caries Research, Department of Pediatric and Preventive Dentistry, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
- Department of Pediatric and Preventive Dentistry, Indira Gandhi Institute of Dental Sciences, Sri Balaji Vidyapeeth, Pondicherry, India
| | - Sneha S Patil
- Department of Environmental Health Engineering, Faculty of Public Health, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
- Department of Pediatric and Preventive Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Sant-Tukaram Nagar, Pimpri, Pune, India
| | - M S Muthu
- Centre for Early Childhood Caries Research, Department of Pediatric and Preventive Dentistry, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - V Vettriselvi
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Selva Arockiam
- Department of Orthodontics, Meenakshi Ammal Dental College and Hospital, Chennai, India
| | - R Kirubakaran
- South Asian Cochrane Network and Centre. Christian Medical College, Vellore, India
| | - N Sivakumar
- Department of Pediatric and Preventive Dentistry, Narayana Dental College and Hospital, Nellore, India
| |
Collapse
|