1
|
Pan S, Zhang Z, Pang W. The causal relationship between bacterial pneumonia and diabetes: a two-sample mendelian randomization study. Islets 2024; 16:2291885. [PMID: 38095344 PMCID: PMC10730180 DOI: 10.1080/19382014.2023.2291885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/03/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Previous observational studies have established the high prevalence of bacterial pneumonia in diabetic patients, which in turn leads to increased mortality. However, the presence of a causal connection between bacterial pneumonia and diabetes remains unobserved. METHODS We chose genome-wide significant (Ρ < 1 × 10-5 and Ρ < 1 × 10-6) and independent (r2 < 0.001) single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) to proceed a bidirectional two-sample MR study. The extracted SNPs explored the relationship between bacterial pneumonia and diabetes by Inverse variance weighted (IVW), MR-Egger, and weighted median methods. In addition, we conducted the Heterogeneity test, the Pleiotropy test, MR-presso and the Leave-one-out (LOO) sensitivity test to validate the reliability of results. RESULTS In an MR study with bacterial pneumonia as an exposure factor, four different types of diabetes as outcome. It was observed that bacterial pneumonia increases the incidence of GDM (OR = 1.150 (1.027-1.274, P = 0.011) and T1DM (OR = 1.277 (1.024-1.531), P = 0.016). In the reverse MR analysis, it was observed that GDM (OR = 1.112 (1.023-1.201, P = 0.009) is associated with an elevated risk of bacterial pneumonia. However, no significant association was observed bacterial pneumonia with T1DM and other types of diabetes (P > 0.05). CONCLUSION This study utilizing MR methodology yields robust evidence supporting a bidirectional causal association between bacterial pneumonia and GDM. Furthermore, our findings suggest a plausible causal link between bacterial pneumonia and T1DM.
Collapse
Affiliation(s)
- Songying Pan
- The School of Public Health, Guilin Medical University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
| | - Zhongqi Zhang
- The School of Public Health, Guilin Medical University, Guilin, Guangxi, China
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
| | - Weiyi Pang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guilin Medical University, Guilin, Guangxi, China
| |
Collapse
|
2
|
Luo P, Guo R, Gao D, Zhang Q. Causal relationship between sex hormones and cutaneous melanoma: a two-sample Mendelian randomized study. Melanoma Res 2024; 34:408-418. [PMID: 38842104 DOI: 10.1097/cmr.0000000000000983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
This study aimed to elucidate the genetic aspects of the relationship between sex hormones and cutaneous melanoma risk, providing valuable insights into this complex association. In this study, we used estradiol, bioavailable testosterone, sex hormone-binding globulin, and total testosterone as the exposure and melanoma as the outcome for two-sample Mendelian randomization analysis. In this study, a random-effects inverse-variance weighting (IVW) model was used as the main analysis model, and the corresponding weighted median, simple mode, weighted mode, and Mendelian randomization‒Egger methods were used as supplementary methods. We assessed both heterogeneity and horizontal pleiotropy in our study, scrutinizing whether the analysis results were affected by any individual single nucleotide polymorphism. The random-effects IVW method indicated that estradiol [odds ratio (OR), 1.000; 95% confidence interval (CI), 0.998-1.003; P = 0.658], bioavailable testosterone (OR = 1.001, 95% CI, 0.999-1.003; P = 0.294), sex hormone-binding globulin (IVW: OR, 1.000; 95% CI, 0.998-1.003; P = 0.658), and total testosterone (IVW: OR, 1.002; 95% CI, 0.999-1.005; P = 0.135) were not genetically linked to cutaneous melanoma. No analyses exhibited heterogeneity, horizontal pleiotropy, or deviations. We were unable to find genetic evidence for a causal relationship between sex hormones and the occurrence of cutaneous melanoma in this study. These results are limited by sample size and population, so the causal relationship between sex hormones and cutaneous melanoma needs to be further studied.
Collapse
Affiliation(s)
- Pan Luo
- Department of Auricular Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | |
Collapse
|
3
|
Delabays B, Trajanoska K, Walonoski J, Mooser V. Cardiovascular Pharmacogenetics: From Discovery of Genetic Association to Clinical Adoption of Derived Test. Pharmacol Rev 2024; 76:791-827. [PMID: 39122647 DOI: 10.1124/pharmrev.123.000750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 04/24/2024] [Accepted: 05/28/2024] [Indexed: 08/12/2024] Open
Abstract
Recent breakthroughs in human genetics and in information technologies have markedly expanded our understanding at the molecular level of the response to drugs, i.e., pharmacogenetics (PGx), across therapy areas. This review is restricted to PGx for cardiovascular (CV) drugs. First, we examined the PGx information in the labels approved by regulatory agencies in Europe, Japan, and North America and related recommendations from expert panels. Out of 221 marketed CV drugs, 36 had PGx information in their labels approved by one or more agencies. The level of annotations and recommendations varied markedly between agencies and expert panels. Clopidogrel is the only CV drug with consistent PGx recommendation (i.e., "actionable"). This situation prompted us to dissect the steps from discovery of a PGx association to clinical translation. We found 101 genome-wide association studies that investigated the response to CV drugs or drug classes. These studies reported significant associations for 48 PGx traits mapping to 306 genes. Six of these 306 genes are mentioned in the corresponding PGx labels or recommendations for CV drugs. Genomic analyses also highlighted the wide between-population differences in risk allele frequencies and the individual load of actionable PGx variants. Given the high attrition rate and the long road to clinical translation, additional work is warranted to identify and validate PGx variants for more CV drugs across diverse populations and to demonstrate the utility of PGx testing. To that end, pre-emptive PGx combining genomic profiling with electronic medical records opens unprecedented opportunities to improve healthcare, for CV diseases and beyond. SIGNIFICANCE STATEMENT: Despite spectacular breakthroughs in human molecular genetics and information technologies, consistent evidence supporting PGx testing in the cardiovascular area is limited to a few drugs. Additional work is warranted to discover and validate new PGx markers and demonstrate their utility. Pre-emptive PGx combining genomic profiling with electronic medical records opens unprecedented opportunities to improve healthcare, for CV diseases and beyond.
Collapse
Affiliation(s)
- Benoît Delabays
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Joshua Walonoski
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| |
Collapse
|
4
|
Héreil A, Guillaume M, Duboscq R, Carretero Y, Pelpoir E, Bitton F, Giraud C, Karlova R, Testerink C, Stevens R, Causse M. Characterisation of a major QTL for sodium accumulation in tomato grown in high salinity. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39148196 DOI: 10.1111/pce.15082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/09/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024]
Abstract
Soil salinity is a serious concern for tomato culture, affecting both yield and quality parameters. Although some genes involved in tomato salt tolerance have been identified, their genetic diversity has been rarely studied. In the present study, we assessed salt tolerance-related traits at juvenile and adult stages in a large core collection and identified salt tolerance quantitative trait loci (QTLs) by genome-wide association study (GWAS). The results suggested that a major QTL is involved in leaf sodium accumulation at both physiological stages. We were able to identify the underlying candidate gene, coding for a well-known sodium transporter, called SlHKT1.2. We showed that an eQTL for the expression of this gene in roots colocalized with the above ground sodium content QTL. A polymorphism putatively responsible for its variation was identified in the gene promoter. Finally, to extend the applicability of these results, we carried out the same analysis on a test-cross panel composed of the core collection crossed with a distant line. The results indicated that the identified QTL retained its functional impact even in a hybrid genetic context: this paves the way for its use in breeding programs aimed at improving salinity tolerance in tomato cultivars.
Collapse
Affiliation(s)
- A Héreil
- UR1052 GAFL, INRAE, Montfavet, France
| | - M Guillaume
- GAUTIER Semences, Route d'Avignon, Eyragues, France
| | - R Duboscq
- UR1052 GAFL, INRAE, Montfavet, France
| | | | - E Pelpoir
- UR1052 GAFL, INRAE, Montfavet, France
| | - F Bitton
- UR1052 GAFL, INRAE, Montfavet, France
| | - C Giraud
- UE A2M, INRAE, Montfavet, France
| | - R Karlova
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, Wageningen, The Netherlands
| | - C Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University & Research, Wageningen, The Netherlands
| | - R Stevens
- UR1052 GAFL, INRAE, Montfavet, France
| | - M Causse
- UR1052 GAFL, INRAE, Montfavet, France
| |
Collapse
|
5
|
Cao Z, Li Q, Wu J, Li Y. Genetic proxies for therapy of insulin drug targets and risk of osteoarthritis: a drug-target Mendelian randomization analysis. Inflammopharmacology 2024:10.1007/s10787-024-01542-8. [PMID: 39127978 DOI: 10.1007/s10787-024-01542-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND The potential effects of insulin therapy on osteoarthritis (OA) risk are poorly understood. This study aimed to explore the causal relationship between insulin therapy and OA. METHODS Mendelian randomization (MR) analysis was performed to examine the association between genetically proxied inhibition of insulin targets and the risk of overall, hip (HOA) and knee OA (KOA). We then performed univariable MR using summary statistics regarding insulin target genes derived from the DrugBank database. Data related to blood glucose reduction levels were used as a proxy for insulin levels. Two phenotypes, type 2 diabetes, and glycosylated hemoglobin levels, were selected as positive controls to confirm the direction and validity of the proxies. The OA datasets were derived from the UK Biobank cohort. Multivariable MR was adjusted for body mass index, sedentary behavior, cigarette smoking, frequency of alcohol intake, age, and genetic sex. RESULTS Genetically proxied insulin therapy was associated with an increased risk of overall OA [odds ratio (OR):1.2595; 95% confidence interval (CI):1.0810-1.4675] and HOA (OR:1.4218; 95%CI:1.1240-1.7985), which remained consistent across multiple MR methods. After adjusting for confounders, we found evidence supporting a significant causal link with a higher risk of overall OA and HOA. A further two-step MR analysis revealed no significant mediation effects from the six mediators in the associations. CONCLUSION There was a causal association between genetically proxied insulin therapy and a higher risk of OA, especially HOA.
Collapse
Affiliation(s)
- Ziqin Cao
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, China
| | - Qiangxiang Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, China
| | - Jianhuang Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, China.
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
| | - Yajia Li
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha, China.
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
| |
Collapse
|
6
|
Lin Z, Zhang Q, Miao Y, Jiang L, Wang A. Causality of inflammatory bowel disease and seborrheic keratosis: A bidirectional two-sample Mendelian randomization study. Skin Res Technol 2024; 30:e13876. [PMID: 39081143 PMCID: PMC11289426 DOI: 10.1111/srt.13876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 07/08/2024] [Indexed: 08/03/2024]
Abstract
BACKGROUND Previous studies have revealed a potential link between inflammatory bowel disease (IBD) and seborrheic keratosis (SK). However, whether this association is causal or confounded remains unknown. METHODS We conducted this two-sample Mendelian randomization (TSMR) analysis to clarify bidirectional causality between IBD, including its two primary conditions Crohn's disease (CD) and ulcerative colitis (UC), and SK. The summary genetic data of IBD, CD, UC and SK were obtained from accessible genome-wide association studies (GWAS). This TSMR study was primarily performed using inverse-variance weighted (IVW) method, complemented by MR-Egger, weighted median (WM), Bayesian weighted MR (BWMR), MR-robust adjusted profile score (MR-RAPS), MR-pleiotropy residual sum and outlier (MR-PRESSO), and radial IVW MR analyses with modified second-order weights (IVW [Mod 2nd]) methods. Assessment of sensitivity and identification of potential outliers were subsequently conducted to aid interpretation of results. RESULTS The forward MR results showed that IBD [odds ratio (OR) = 1.068, 95% confidence interval (CI) = 1.010-1.129, p = 0.020) and its subtype CD (OR = 1.088, 95%CI = 1.038-1.139, p < 0.001) increased the risk of SK. However, the occurrence of SK could not be affected by UC (OR = 1.090, 95%CI = 0.977-1.216, p = 0.123). In the reverse analysis, no causal relationship between SK and IBD (OR = 0.905, 95%CI = 0.813-1.008, p = 0.069), UC (OR = 0.959, 95%CI = 0.860-1.068, p = 0.443), and CD (OR = 0.933, 95%CI = 0.846-1.029, p = 0.165) was identified. CONCLUSION These findings demonstrate that IBD and its subtype CD could increase the incidence of SK in European populations, whereas SK does not affect IBD occurrence.
Collapse
Affiliation(s)
- Zhipeng Lin
- Department of DermatologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Qi Zhang
- Department of DermatologyThe Second Hospital of Dalian Medical UniversityDalianChina
- Department of DermatologyDalian Third People's Hospital Affiliated to Dalian Medical UniversityDalianChina
| | - Yu Miao
- Department of DermatologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Lin Jiang
- Department of DermatologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | - Aoxue Wang
- Department of DermatologyThe Second Hospital of Dalian Medical UniversityDalianChina
| |
Collapse
|
7
|
Xiang Y, Zhang C, Wang J, Cheng Y, Wang K, Wang L, Tong Y, Yan D. Role of blood metabolites in mediating the effect of gut microbiome on the mutated-RAS/BRAF metastatic colorectal cancer-specific survival. Int J Colorectal Dis 2024; 39:116. [PMID: 39046546 PMCID: PMC11269474 DOI: 10.1007/s00384-024-04686-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/09/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Recent studies have linked alterations in the gut microbiome and metabolic disruptions to the invasive behavior and metastasis of colorectal cancer (CRC), thus affecting patient prognosis. However, the specific relationship among gut microbiome, metabolite profiles, and mutated-RAS/BRAF metastatic colorectal cancer (M-mCRC) remains unclear. Furthermore, the potential mechanisms and prognostic implications of metabolic changes induced by gut microbiome alterations in patients with M-mCRC still need to be better understood. METHODS We conducted Mendelian randomization (MR) to evaluate the causal relationship of genetically predicted 196 gut microbiome features and 1400 plasma metabolites/metabolite ratios on M-mCRC-specific survival. Additionally, we identified significant gut microbiome-metabolites/metabolite ratio associations based on M-mCRC. Metabolite information was annotated, and functional annotation and pathway enrichment analyses were performed on shared proteins corresponding to significant metabolite ratios, aiming to reveal potential mechanisms by which gut microbiome influences M-mCRC prognosis via modulation of human metabolism. RESULTS We identified 11 gut microbiome features and 49 known metabolites/metabolite ratios correlated with M-mCRC-specific survival. Furthermore, we identified 17 gut microbiome-metabolite/metabolite ratio associations specific to M-mCRC, involving eight lipid metabolites and three bilirubin degradation products. The shared proteins corresponding to significant metabolite ratios were predominantly localized within the integral component of the membrane and exhibited enzymatic activities such as glucuronosyltransferase and UDP-glucuronosyltransferase, crucial in processes such as glucuronidation, bile secretion, and lipid metabolism. Moreover, these proteins were significantly enriched in pathways related to ascorbate and aldarate metabolism, pentose and glucuronate interconversions, steroid hormone biosynthesis, and bile secretion. CONCLUSION Our study offers novel insights into the potential mechanisms underlying the impact of the gut microbiome on the prognosis of M-mCRC. These findings serve as a meaningful reference for exploring potential therapeutic targets and strategies in the future.
Collapse
Affiliation(s)
- Yaoxian Xiang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Chan Zhang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Jing Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Yurong Cheng
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Kangjie Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Li Wang
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Yingying Tong
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China
| | - Dong Yan
- Department of Oncology, Beijing Luhe Hospital Affiliated to Capital Medical University, Beijing, 101149, China.
| |
Collapse
|
8
|
Liu H, Zhang X, Shang Y, Zhao S, Li Y, Zhou X, Huo X, Qiao P, Wang X, Dai K, Li H, Guo J, Shi W. Genome-wide association study reveals genetic loci for ten trace elements in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:186. [PMID: 39017920 DOI: 10.1007/s00122-024-04690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
KEY MESSAGE One hundred and fifty-five QTL for trace element concentrations in foxtail millet were identified using a genome-wide association study, and a candidate gene associated with Ni-Co-Cr concentrations was detected. Foxtail millet (Setaria italica) is an important regional crop known for its rich mineral nutrient content, which has beneficial effects on human health. We assessed the concentrations of ten trace elements (Ba, Co, Cr, Cu, Fe, Mn, Ni, Pb, Sr, and Zn) in the grain of 408 foxtail millet accessions. Significant differences in the concentrations of five elements (Ba, Co, Ni, Sr, and Zn) were observed between two subpopulations of spring- and summer-sown foxtail millet varieties. Moreover, 84.4% of the element pairs exhibited significant correlations. To identify the genetic factors influencing trace element accumulation, a comprehensive genome-wide association study was conducted, identifying 155 quantitative trait locus (QTL) for the ten trace elements across three different environments. Among them, ten QTL were consistently detected in multiple environments, including qZn2.1, qZn4.4, qCr4.1, qFe6.3, qFe6.5, qCo6.1, qPb7.3, qPb7.5, qBa9.1, and qNi9.1. Thirteen QTL clusters were detected for multiple elements, which partially explained the correlations between elements. Additionally, the different concentrations of five elements between foxtail millet subpopulations were caused by the different frequencies of high-concentration alleles associated with important marker-trait associations. Haplotype analysis identified a candidate gene SETIT_036676mg associated with Ni accumulation, with the GG haplotype significantly increasing Ni-Co-Cr concentrations in foxtail millet. A cleaved amplified polymorphic sequence marker (cNi6676) based on the two haplotypes of SETIT_036676mg was developed and validated. Results of this study provide valuable reference information for the genetic research and improvement of trace element content in foxtail millet.
Collapse
Affiliation(s)
- Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Zhang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yuping Shang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Shaoxing Zhao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yingjia Li
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xutao Zhou
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xiaoyu Huo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Xin Wang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Huixia Li
- Millet Research Institute, Shanxi Agricultural University, Changzhi, 046000, China
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Weiping Shi
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, 030801, China.
| |
Collapse
|
9
|
Gao N, Yu Z, Fan Y, Jiang X, Hu T. Impact of negative emotions on upper gastrointestinal diseases: A Mendel randomization study. PLoS One 2024; 19:e0304121. [PMID: 38995968 PMCID: PMC11244763 DOI: 10.1371/journal.pone.0304121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 05/07/2024] [Indexed: 07/14/2024] Open
Abstract
Mendelian randomization method is a powerful tool in epidemiological research. The core idea is to use genetic variation as a tool to assess the causal relationship between risk factors and specific diseases. Confounding factors are important interference factors for causal inference in epidemiological studies, and genetic variation in Mendelian randomization studies follows the principle of random distribution of alleles to offspring, which is similar to randomized controlled trials. Mendel 's randomization method can effectively avoid the confounding factors, reverse causality in observational studies and the representativeness and feasibility of randomized controlled trials. Previous observational studies have reported a relationship between negative emotions and upper gastrointestinal disease. However, whether this relationship is causal remains unclear. We aimed to evaluate the causal relationship between negative emotions and upper gastrointestinal diseases using two-sample Mendelian randomization (MR). Three sets of genetic instruments from the database were obtained for analysis, including 12 anxiety-related single nucleotide polymorphisms (SNPs), 46 depression-related SNPs, and 58 nervous-related SNPs. SNPs were filtered using the Phenoscanner website, and the inverse variance weighted method, weighted median method, MR-Egger regression, MR pleiotropy residual sum, and outlier test were used for analysis. In inverse variance weighted analysis, anxiety and depression had an effect on gastroduodenal ulcer (p = 2.849×10-3, β = 4.908, 95% CI = 1.684-8.132; and p = 6.457×10-4, β = 1.767, 95% CI = 0.752-2.782, respectively). Additionally, depression had an effect on diseases of the esophagus, stomach, and duodenum (p = 3.498×10-5, β = 0.926, 95% CI = 0.487-1.364). Cochran's Q-derived p-values were 0.457, 0.603, and 0.643, and MR-Egger intercept-derived p-values were 0.697, 0.294, and 0.362, respectively. Here, we show that anxiety and depression have a causal relationship with gastroduodenal ulcers, and depression has a causal relationship with diseases of the esophagus, stomach, and duodenum.
Collapse
Affiliation(s)
- Nan Gao
- Changchun University of Chinese Medicine, Changchun, China
| | - Zhun Yu
- Changchun University of Chinese Medicine, Changchun, China
| | - Yu Fan
- Changchun University of Chinese Medicine, Changchun, China
| | - Xue Jiang
- Changchun University of Chinese Medicine, Changchun, China
| | - Ting Hu
- Changchun University of Chinese Medicine, Changchun, China
| |
Collapse
|
10
|
Yan J, Li B, Luo C. Gut microbiota's role in glioblastoma risk, with a focus on the mediating role of metabolites. Front Neurol 2024; 15:1386885. [PMID: 39022732 PMCID: PMC11253649 DOI: 10.3389/fneur.2024.1386885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024] Open
Abstract
This study employed Mendelian randomization (MR) analysis to systematically investigate the potential connections between gut microbiota and the risk of glioblastoma (GBM). We identified 12 microbial groups closely associated with the incidence risk of GBM. Subsequently, MR analysis was conducted on 1,091 blood metabolites and 309 metabolite ratios, revealing 19 metabolites that exert an impact on the occurrence of GBM. Hypothesizing that gut microbiota may influence the risk of glioblastoma multiforme by modulating these metabolites, we performed MR analyses, considering each microbial group as exposure and each metabolite as an outcome. Through these analyses, we constructed a regulatory network encompassing gut microbiota, metabolites, and GBM, providing a novel perspective for a deeper understanding of the role of the gut-brain axis in the pathogenesis of GBM. This research offers crucial insights into how gut microbiota may affect the risk of GBM by regulating specific metabolites. The identified regulatory network of the gut-brain axis may play a significant role in the formation and development of GBM, providing valuable information for future research and therapeutic interventions.
Collapse
Affiliation(s)
- Junqing Yan
- Nanxiang Branch of Ruijin Hospital, Shanghai, China
| | - Bo Li
- Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai, China
| | - Chun Luo
- Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai, China
| |
Collapse
|
11
|
Han X, Yang Q, Lu Y, Xu M, Tao Q, Jiang S, He X, Bai Y, Zhang T, Bai L, Hu J, Zhu Y, Liu H, Li L. Genome-wide association study reveals the candidate genes of humerus quality in laying duck. Poult Sci 2024; 103:103851. [PMID: 38806002 PMCID: PMC11154710 DOI: 10.1016/j.psj.2024.103851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024] Open
Abstract
Bone plays a crucial role in poultry's health and production. However, during the selection and cage farming, there has been a decline in bone quality. As the development of breeding theory, researchers find that it's possible to enhance bone quality through selective breeding.This study measure 8 humerus quality in 260 samples of the 350-day-old female duck. By descripting the basic characteristic traits, mechanical property traits we found that all the bone quality traits had a large variable coefficient, especially mechanical properties trait (20-70%), indicating that there was a large difference in bone health status among laying ducks. The phenotypic correlations showed a high correlation between weight and density, diameter and perimeter, breaking and toughness (r = 0.52-0.68). And then, we performed the Genome-wide association study (GWAS) to reveal the candidate genes of humerus quality in ducks. Seven candidate protein-coding genes were identified with perimeter trait, and 52 protein-coding genes were associated with toughness trait. We also analysed the candidate region and performed KEGG and GO analyse for 75 candidate genes. Furthermore, the expression analyse of the above candidate genes in different stage of humerus and different tissues were performed. Finally, AP2A2, SMAD3, SMNDC1, NFIA, EPHB2, PMEPA1, UNC5C, ESR1, VAV3, NFATC2 deserve further focus. The obtained results can contribute to new insight into bone quality and provide new genetic biomarkers for application in duck breeding programs.
Collapse
Affiliation(s)
- Xu Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Qinglan Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yinjuan Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Mengru Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Qiuyu Tao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Shuaixue Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Xinxin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yuan Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Tao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Lili Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Jiwei Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Yuanchun Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - HeHe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, PR China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, PR China.
| |
Collapse
|
12
|
Li YT, Zeng X. Circulating inflammatory cytokines influencing schizophrenia: a Mendelian randomization study. Front Psychiatry 2024; 15:1417213. [PMID: 38979494 PMCID: PMC11228335 DOI: 10.3389/fpsyt.2024.1417213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Introduction Schizophrenia (SCZ) is a severe psychiatric disorder whose pathophysiology remains elusive. Recent investigations have underscored the significance of systemic inflammation, particularly the impact of circulating inflammatory proteins, in SCZ. Methods This study explores the potential causal association between certain inflammatory proteins and SCZ. Bidirectional Mendelian randomization (MR) analyses were conducted utilizing data from expansive genome-wide association studies (GWAS). Data regarding circulating inflammatory proteins were sourced from the GWAS Catalog database, encompassing 91 inflammatory cytokines. SCZ-related data were derived from the Finngen database, incorporating 47,696 cases and 359,290 controls. Analytical methods such as inverse variance weighted, MR-Egger, weighted median, simple mode, and weighted mode were employed to evaluate the association between inflammatory cytokines and SCZ. Sensitivity analyses were also performed to affirm the robustness of the results. Results Following FDR adjustment, significant associations were observed between levels of inflammatory cytokines, including Fibroblast Growth Factor 5 (OR = 1.140, 95%CI = 1.045, 1.243, p = 0.003, FDR=0.015), C-C Motif Chemokine 4 (OR = 0.888, 95%CI = 0.816, 0.967, p = 0.006, FDR = 0.015), C-X-C Motif Chemokine 1 (OR = 0.833, 95%CI = 0.721, 0.962, p = 0.013, FDR = 0.064), and C-X-C Motif Chemokine 5 (OR = 0.870, 95%CI = 0.778, 0.973, p = 0.015, FDR = 0.074), and the risk of SCZ. Conclusion Our results from MR analysis suggest a potential causal link between circulating inflammatory cytokines and SCZ, thereby enriching our understanding of the interactions between inflammation and SCZ. Furthermore, these insights provide a valuable foundation for devising therapeutic strategies targeting inflammation.
Collapse
Affiliation(s)
- Yao-Ting Li
- Department of Forensic Science, Guangdong Police College, Guangzhou, Guangdong, China
| | - Xuezhen Zeng
- Department of Pharmacy, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
13
|
Xu S, Fang H, Shen T, Zhou Y, Zhang D, Ke Y, Chen Z, Lu Z. Causal association between immune cells and lung cancer risk: a two-sample bidirectional Mendelian randomization analysis. Front Immunol 2024; 15:1433299. [PMID: 38962009 PMCID: PMC11219561 DOI: 10.3389/fimmu.2024.1433299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
Background Previous studies have highlighted the crucial role of immune cells in lung cancer development; however, the direct link between immunophenotypes and lung cancer remains underexplored. Methods We applied two-sample Mendelian randomization (MR) analysis, using genetic variants as instruments to determine the causal influence of exposures on outcomes. This method, unlike traditional randomized controlled trials (RCTs), leverages genetic variants inherited randomly at conception, thus reducing confounding and preventing reverse causation. Our analysis involved three genome-wide association studies to assess the causal impact of 731 immune cell signatures on lung cancer using genetic instrumental variables (IVs). We initially used the standard inverse variance weighted (IVW) method and further validated our findings with three supplementary MR techniques (MR-Egger, weighted median, and MR-PRESSO) to ensure robustness. We also conducted MR-Egger intercept and Cochran's Q tests to assess heterogeneity and pleiotropy. Additionally, reverse MR analysis was performed to explore potential causality between lung cancer subtypes and identified immunophenotypes, using R software for all statistical calculations. Results Our MR analysis identified 106 immune signatures significantly associated with lung cancer. Notably, we found five suggestive associations across all sensitivity tests (P<0.05): CD25 on IgD- CD24- cells in small cell lung carcinoma (ORIVW =0.885; 95% CI: 0.798-0.983; P IVW =0.022); CD27 on IgD+ CD24+ cells in lung squamous cell carcinoma (ORIVW =1.054; 95% CI: 1.010-1.100; P IVW =0.015); CCR2 on monocyte cells in lung squamous cell carcinoma (ORIVW =0.941; 95% CI: 0.898-0.987; P IVW =0.012); CD123 on CD62L+ plasmacytoid dendritic cells (ORIVW =0.958; 95% CI: 0.924-0.992; P IVW =0.017) as well as on plasmacytoid dendritic cells (ORIVW =0.958; 95% CI: 0.924-0.992; P IVW =0.017) in lung squamous cell carcinoma. Conclusion This study establishes a significant genomic link between immune cells and lung cancer, providing a robust basis for future clinical research aimed at lung cancer management.
Collapse
Affiliation(s)
- Shengshan Xu
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Huiying Fang
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC), Chongqing University Cancer Hospital, Chongqing, China
| | - Tao Shen
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Yufu Zhou
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Dongxi Zhang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Yongwen Ke
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Zhuowen Chen
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Zhuming Lu
- Department of Thoracic Surgery, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| |
Collapse
|
14
|
Li M, Shi P, Yang H, Liu S, Sun R, Li L, Zhao Z, Sun J. The immune cells have complex causal regulation effects on cancers. Int Immunopharmacol 2024; 134:112179. [PMID: 38710118 DOI: 10.1016/j.intimp.2024.112179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND There was a large body of evidence linking immune cells to cancer risk. However, the causal relationship between immune cells, cancer, and what genes play an important role is unclear. METHODS In this study, we performed comprehensive two-sample Mendelian randomization analysis (TSMR) to determine the causal relationship between immune cells and common cancers. We also performed Multimarker Analysis of Genomic Annotation (MAGMA) on immune cells causally associated with cancer to identify their relevant genes and used data summary-based MR (SMR) analysis to investigate the causal relationship between their gene expression, methylation, and cancer, and further used drug prediction and molecular docking to validate the medicinal value of the targets. Finally, reverse TSMR analysis was performed on cancer and immune cells to rule out reverse causality. RESULTS After FDR correction (PFDR < 0.05), the results showed that 2 immune cells were associated with lung cancer risk, and 1 immune cell was significantly associated with pancreatic cancer risk. The expression of OSBPL10, CHD4, SMDT1, PHETA2, and NAGA was positively and causally related to the risk of lung cancer by SMR analysis and HEIDI test. We also found that increased expression of ANP32E decreased the risk of pancreatic cancer and that the methylation level of OSBPL10, CHD4, SULF2, CENPM, and CYP2D6 had a causal association with lung cancer. The methylation level of FCGR3A was causally associated with pancreatic cancer. The results of molecular docking indicated a strong affinity between the drugs and proteins that possessed existing structural information. CONCLUSION This data-driven Mendelian randomization (MR) study demonstrates the causal role of immune cells in cancers. In addition, this study identifies candidate genes that may be potential anti-cancer drug targets.
Collapse
Affiliation(s)
- Mingzheng Li
- Department of Environmental and Occupational Health, School of Public Health, China Medical University, Shenyang 110122, China
| | - Peng Shi
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Huajie Yang
- Department of Environmental and Occupational Health, School of Public Health, China Medical University, Shenyang 110122, China
| | - Shuailing Liu
- Institute for International Health Professions Education and Research, China Medical University, Shenyang 110122, China; College of Health Management, China Medical University, Shenyang 110122, China
| | - Ruixi Sun
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Luoxin Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Zetong Zhao
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Jiaxing Sun
- Ultrasound Department, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China.
| |
Collapse
|
15
|
Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
Collapse
Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
16
|
Yao T, Lin YL, Wu YQ, Qian XG, Wang ZN, Qian S, Jiang T, Liu JC, Fang LX, Zhen C, Wu CH. Identifying therapeutic targets for breast cancer: insights from systematic Mendelian randomization analysis. Front Oncol 2024; 14:1407795. [PMID: 38887235 PMCID: PMC11180768 DOI: 10.3389/fonc.2024.1407795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Background Breast cancer (BC) exhibits a high incidence rate, imposing a substantial burden on healthcare systems. Novel drug targets are urgently needed for BC. Mendelian randomization (MR) has gained widespread application for identifying fresh therapeutic targets. Our endeavor was to pinpoint circulatory proteins causally linked to BC risk and proffer potential treatment targets for BC. Methods Through amalgamating protein quantitative trait loci from 2,004 circulating proteins and comprehensive genome-wide association study data from the Breast Cancer Association Consortium, we conducted MR analyses. Employing Steiger filtering, bidirectional MR, Bayesian colocalization, phenotype scanning, and replication analyses, we further solidified MR study outcomes. Additionally, protein-protein interaction (PPI) network was harnessed to unveil latent associations between proteins and prevailing breast cancer medications. The phenome-wide MR (Phe-MR) was employed to assess potential side effects and indications for the druggable proteins of BC. Finally, we further affirmed the drugability of potential drug targets through mRNA expression analysis and molecular docking. Results Through comprehensive analysis, we identified five potential drug targets, comprising four (TLR1, A4GALT, SNUPN, and CTSF) for BC and one (TLR1) for BC_estrogen receptor positive. None of these five potential drug targets displayed reverse causation. Bayesian colocalization suggested that these five latent drug targets shared variability with breast cancer. All drug targets were replicated within the deCODE cohort. TLR1 exhibited PPI with current breast cancer therapeutic targets. Furthermore, Phe-MR unveiled certain adverse effects solely for TLR1 and SNUPN. Conclusion Our study uncovers five prospective drug targets for BC and its subtypes, warranting further clinical exploration.
Collapse
Affiliation(s)
- Tao Yao
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yun-Lu Lin
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yu-Qing Wu
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xin-Ge Qian
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhe-Ning Wang
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Sang Qian
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ting Jiang
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jing-Chen Liu
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Luo-Xiang Fang
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Cheng Zhen
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chun-Hui Wu
- Children’s Heart Center, The Second Affiliated Hospital and Yuying Children’s Hospital, Institute of Cardiovascular Development and Translational Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| |
Collapse
|
17
|
Luo P, Gao D, Zhang Q. Genetic causal relationship between gut microbiota and basal cell carcinoma: A two-sample mendelian randomization study. Skin Res Technol 2024; 30:e13804. [PMID: 38895789 PMCID: PMC11187847 DOI: 10.1111/srt.13804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
OBJECTIVE Research has previously established connections between the intestinal microbiome and the progression of some cancers. However, there is a noticeable gap in the literature in regard to using Mendelian randomisation (MR) to delve into potential causal relationships between the gut microbiota (GM) and basal cell carcinoma (BCC). Therefore, the purpose of our study was to use MR to explore the causal relationship between four kinds of GM (Bacteroides, Streptococcus, Proteobacteria and Lachnospiraceae) and BCC. METHODS We used genome-wide association study (GWAS) data and MR to explore the causal relationship between four kinds of GM and BCC. This study primarily employed the random effect inverse variance weighted (IVW) model for analysis, as complemented by additional methods including the simple mode, weighted median, weighted mode and MR‒Egger methods. We used heterogeneity and horizontal multiplicity to judge the reliability of each analysis. MR-PRESSO was mainly used to detect and correct outliers. RESULTS The random-effects IVW results showed that Bacteroides (OR = 0.936, 95% CI = 0.787-1.113, p = 0.455), Streptococcus (OR = 0.974, 95% CI = 0.875-1.083, p = 0.629), Proteobacteria (OR = 1.113, 95% CI = 0.977-1.267, p = 0.106) and Lachnospiraceae (OR = 1.027, 95% CI = 0.899-1.173, p = 0.688) had no genetic causal relationship with BCC. All analyses revealed no horizontal pleiotropy, heterogeneity or outliers. CONCLUSION We found that Bacteroides, Streptococcus, Proteobacteria and Lachnospiraceae do not increase the incidence of BCC at the genetic level, which provides new insight for the study of GM and BCC.
Collapse
Affiliation(s)
- Pan Luo
- Department of Comprehensive Plastic SurgeryPlastic Surgery HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Dejin Gao
- Department of Comprehensive Plastic SurgeryPlastic Surgery HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Qingguo Zhang
- Department of Comprehensive Plastic SurgeryPlastic Surgery HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| |
Collapse
|
18
|
Wang P, Liu T, Zhang Q, Luo P. Genetic causal relationship between gut microbiota and cutaneous melanoma: a two-sample Mendelian randomization study. Melanoma Res 2024; 34:225-233. [PMID: 38469881 DOI: 10.1097/cmr.0000000000000960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Currently, numerous studies suggest a potential association between the gut microbiota and the progression of melanoma. Hence, our objective was to examine the genetic impact of the gut microbiota on melanoma through the utilization of the Mendelian randomization (MR) approach. This research employed Bacteroides, Streptococcus, Proteobacteria, and Lachnospiraceae as exposure variables and cutaneous melanoma (CM) as the outcome in a two-sample MR analysis. In this MR research, the primary analytical approach was the random-effects inverse-variance weighting (IVW) model. Complementary methods included weighted median, MR Egger, and basic and weighted models. We assessed both heterogeneity and horizontal pleiotropy in our study, scrutinizing whether the analysis results were affected by any individual SNP. The random-effects IVW outcomes indicated that Streptococcus, Bacteroides, Lachnospiraceae and Proteobacteria had no causal relationship with CM, with odds ratios of 1.001 [95% confidence interval (CI) = 0.998-1.004, P = 0.444], 0.999 (95% CI = 0.996-1.002, P = 0.692), 1.001 (95% CI = 0.998-1.003, P = 0.306), and 0.999 (95% CI = 0.997-1.002, P = 0.998), respectively. No analyses exhibited heterogeneity, horizontal pleiotropy, or deviations. Our research determined that Bacteroides, Streptococcus, Proteobacteria, and Lachnospiraceae do not induce CM at the genetic level. However, we cannot dismiss the possibility that these four gut microbiotas might influence CM through other mechanisms.
Collapse
Affiliation(s)
- Peizhou Wang
- Department of Auricular Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | |
Collapse
|
19
|
Nie D, He X, Zheng H, Deng D, He F, Li R, Ni X, Li S, Xu F. Association between green tea intake and digestive system cancer risk in European and East Asian populations: a Mendelian randomization study. Eur J Nutr 2024; 63:1103-1111. [PMID: 38319384 DOI: 10.1007/s00394-023-03312-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/18/2023] [Indexed: 02/07/2024]
Abstract
PURPOSE Previous observational studies have shown that green tea consumption is associated with a reduced incidence of digestive system cancers (DSCs). However, the observed association could be due to confounding factors. Therefore, we used a two-sample Mendelian randomization (MR) approach to assess the causal effect of green tea intake on the risk of five common DSCs. METHODS Independent genetic variants strongly associated with green tea consumption in European and East Asian populations were selected as instrumental variables in genome-wide association studies involving up to 64,949 European individuals and 152,653 East Asian individuals, respectively. The associations between genetic variants and DSCs were extracted from the FinnGen study and the Japan Biobank. The primary analysis was performed using random-effects inverse variance weighting (IVW). Other MR analyses, including weighted mode-based estimate, weighted-median, MR-Egger regression, Mendelian Randomization-Pleiotropy Residual Sum and Outlier (MR-PRESSO) analysis, were used for sensitivity analyses. In addition, a multivariate MR design was performed to adjust for smoking and alcohol consumption. RESULTS The IVW results showed no causal relationship between tea intake and DSCs risk in European population (esophagus cancer: odds ratio (OR) = 1.044, 95% confidence interval (CI) 0.992-1.099, p = 0.096; stomach cancer: OR = 0.988, 95% CI 0.963-1.014, p = 0.368; colorectal cancer: OR = 1.003, 95% CI 0.992-1.015, p = 0.588; liver cancer: OR = 0.996, 95% CI 0.960-1.032, p = 0.808; pancreatic cancer: OR = 0.990, 95% CI 0.965-1.015, p = 0.432). The MR-Egger regression, MR-PRESSO analysis and other methods also confirmed the reliability of the conclusion. Similarly, no significant association was found between green tea consumption and the incidence of DSCs among East Asians. This relationship is not significant even after adjusting for smoking and alcohol consumption (P > 0.05). CONCLUSION Our study provides evidence that genetically predicted green tea intake is not causally associated with the development of DSCs in the European and East Asian population.
Collapse
Affiliation(s)
- Duorui Nie
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaoyu He
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hao Zheng
- First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Deyu Deng
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Fanghui He
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Ruyi Li
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaoting Ni
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Shunxiang Li
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China.
- Hunan Engineering Technology Research Center for Bioactive Substance Discovery of Chinese Medicine, Changsha, China.
- Hunan Province Sino-US International Joint Research Center for Therapeutic Drugs of Senile Degenerative Diseases, Changsha, China.
| | - Fei Xu
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China.
- Hunan Engineering Technology Research Center for Bioactive Substance Discovery of Chinese Medicine, Changsha, China.
- Hunan Province Sino-US International Joint Research Center for Therapeutic Drugs of Senile Degenerative Diseases, Changsha, China.
| |
Collapse
|
20
|
Ran Z, Zheng Y, Yu L, Zhang Y, Zhang Z, Li H, Li X, Song J, Zhang L, Zhang R, Lu C, Gong Y, Gong J. Linking artificial sweetener intake with kidney function: insights from NHANES 2003-2006 and findings from Mendelian randomization research. Front Nutr 2024; 11:1387676. [PMID: 38873559 PMCID: PMC11169671 DOI: 10.3389/fnut.2024.1387676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/29/2024] [Indexed: 06/15/2024] Open
Abstract
Background The current investigation examines the association between artificial sweetener (AS) consumption and the likelihood of developing chronic kidney disease (CKD), along with its impact on kidney function. Methods We utilized data from the National Health and Nutrition Examination Survey from 2003-2006 to conduct covariance analysis and weighted adjusted logistic regression, aiming to assess the association between artificial sweetener intake and CKD risk, as well as kidney function indicators. Subsequently, we employed Mendelian randomization methods to validate the causal relationship between the intake of artificial sweeteners, CKD risk, and kidney function indicators. Instrumental variable analysis using inverse-variance weighting and Robust adjusted profile score were the primary analytical methods employed. Results A total of 20,470 participants were included in the study, with 1,257 participants ultimately included in the analysis. In all adjusted logistic regression models, no significant association was found between the intake of artificial sweeteners and CKD risk. Similarly, the summary odds ratios (OR) for each unit change in genetically predicted CKD risk were 2.14 (95% CI: 0.83, 5.21, p = 0.092), 1.41 (95% CI: 0.54, 3.63, p = 0.482), and 1.50 (95% CI: 0.50, 4.52, p = 0.468) for the impact of artificial sweeteners added to cereals, tea, and coffee, respectively. It was only observed that adding artificial sweeteners to coffee was associated with a modest reduction in urinary albumin-to-creatinine ratio (OR = 0.94, 95% CI: -0.108, -0.022, p = 0.003), the effect appeared to be relatively small and may not directly impact the individual level. Conclusion Our study does not support a causal relationship between artificial sweetener intake and the risk of CKD. However, due to the limitations and potential confounding factors, these findings need to be further validated through larger sample sizes in observational studies and Mendelian randomization analyses.
Collapse
Affiliation(s)
- Zhuoling Ran
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuxuan Zheng
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Lin Yu
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuxian Zhang
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Zhenjiang Zhang
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Huijie Li
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Xuhan Li
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Jing Song
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Li Zhang
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Ran Zhang
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Chang Lu
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Yang Gong
- McWilliams School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, United States
| | - Jian Gong
- Research Group of Jian Gong on Pharmacoepidemiology and Clinical Drug Evaluation, School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| |
Collapse
|
21
|
Hou Y, Xiao Z, Zhu Y, Li Y, Liu Q, Wang Z. Blood metabolites and chronic kidney disease: a Mendelian randomization study. BMC Med Genomics 2024; 17:147. [PMID: 38807172 PMCID: PMC11131213 DOI: 10.1186/s12920-024-01918-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Human blood metabolites have demonstrated close associations with chronic kidney disease (CKD) in observational studies. Nonetheless, the causal relationship between metabolites and CKD is still unclear. This study aimed to assess the associations between metabolites and CKD risk. METHODS We applied a two-sample Mendelian randomization (MR) analysis to evaluate relationships between 1400 blood metabolites and eight phenotypes (outcomes) (CKD, estimated glomerular filtration rate(eGFR), urine albumin to creatinine ratio, rapid progress to CKD, rapid decline of eGFR, membranous nephropathy, immunoglobulin A nephropathy, and diabetic nephropathy). The inverse variance weighted (IVW), MR-Egger, and weighted median were used to investigate the causal relationship. Sensitivity analyses were performed with Cochran's Q, MR-Egger intercept, MR-PRESSO Global test, and leave-one-out analysis. Bonferroni correction was used to test the strength of the causal relationship. RESULTS Through the MR analysis of 1400 metabolites and eight clinical phenotypes, a total of 48 metabolites were found to be associated with various outcomes. Among them, N-acetylleucine (OR = 0.923, 95%CI: 0.89-0.957, PIVW = 1.450 × 10-5) has a strong causal relationship with lower risk of CKD after the Bonferroni-corrected test, whereas Glycine to alanine ratio has a strong causal relationship with higher risk of CKD (OR = 1.106, 95%CI: 1.063-1.151, PIVW = 5.850 × 10-7). No horizontal pleiotropy and heterogeneity were detected. CONCLUSION Our study offers groundbreaking insights into the integration of metabolomics and genomics to reveal the pathogenesis of and therapeutic strategies for CKD. It underscores 48 metabolites as potential causal candidates, meriting further investigation.
Collapse
Affiliation(s)
- Yawei Hou
- Institute of Chinese Medical Literature and Culture, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhenwei Xiao
- Department of Nephrology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yushuo Zhu
- Department of Emergency and Critical Care Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yameng Li
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qinglin Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhenguo Wang
- Institute of Chinese Medical Literature and Culture, Shandong University of Traditional Chinese Medicine, Jinan, China.
| |
Collapse
|
22
|
Downie CG, Highland HM, Alotaibi M, Welch BM, Howard AG, Cheng S, Miller N, Jain M, Kaplan RC, Lilly AG, Long T, Sofer T, Thyagarajan B, Yu B, North KE, Avery CL. Genome-wide association study reveals shared and distinct genetic architecture underlying fatty acid and bioactive oxylipin metabolites in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24307719. [PMID: 38826448 PMCID: PMC11142272 DOI: 10.1101/2024.05.21.24307719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Bioactive fatty acid-derived oxylipin molecules play key roles in mediating inflammation and oxidative stress, which underlie many chronic diseases. Circulating levels of fatty acids and oxylipins are influenced by both environmental and genetic factors; characterizing the genetic architecture of bioactive lipids could yield new insights into underlying biological pathways. Thus, we performed a genome wide association study (GWAS) of n=81 fatty acids and oxylipins in n=11,584 Hispanic Community Health Study/Study of Latinos (HCHS/SOL) participants with genetic and lipidomic data measured at study baseline (58.6% female, mean age = 46.1 years, standard deviation = 13.8 years). Additionally, given the effects of central obesity on inflammation, we examined interactions with waist circumference using two-degree-of-freedom joint tests. Heritability estimates ranged from 0% to 47.9%, and 48 of the 81oxylipins and fatty acids were significantly heritable. Moreover, 40 (49.4%) of the 81 oxylipins and fatty acids had at least one genome-wide significant (p< 6.94E-11) variant resulting in 19 independent genetic loci involved in fatty acid and oxylipin synthesis, as well as downstream pathways. Four loci (lead variant minor allele frequency [MAF] range: 0.08-0.50), including the desaturase-encoding FADS and the OATP1B1 transporter protein-encoding SLCO1B1, exhibited associations with four or more fatty acids and oxylipins. The majority of the 15 remaining loci (87.5%) (lead variant MAF range = 0.03-0.45, mean = 0.23) were only associated with one oxylipin or fatty acid, demonstrating evidence of distinct genetic effects. Finally, while most loci identified in two-degree-of-freedom tests were previously identified in our main effects analyses, we also identified an additional rare variant (MAF = 0.002) near CARS2, a locus previously implicated in inflammation. Our analyses revealed shared and distinct genetic architecture underlying fatty acids and oxylipins, providing insights into genetic factors and motivating future multi-omics work to characterize these compounds and elucidate their roles in disease pathways.
Collapse
Affiliation(s)
- Carolina G Downie
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, San Diego, CA
| | - Barrett M Welch
- School of Public Health, University of Nevada, Reno, Reno, NV
| | - Annie Green Howard
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Mohit Jain
- Sapient Bioanalytics, San Diego, CA
- Departments of Medicine and Pharmacology, University of California, San Diego, San Diego, CA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY; Public Health Sciences Division, Fred Hutchison Cancer Center, Seattle, WA
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tao Long
- Sapient Bioanalytics, San Diego, CA
| | - Tamar Sofer
- CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis, MN
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| |
Collapse
|
23
|
Li Z, Teng Z, Han Z, Zhang Y, Wang Y. Genetically predicted asthma and the risk of abnormal spermatozoa. Front Genet 2024; 15:1377770. [PMID: 38846962 PMCID: PMC11153665 DOI: 10.3389/fgene.2024.1377770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 05/01/2024] [Indexed: 06/09/2024] Open
Abstract
Background Several previous animal and human studies have found a strong association between asthma and spermatozoa quality, but whether these associations are causal or due to bias remains to be elucidated. Methods We performed a two-sample Mendelian randomization (MR) analysis to assess the causal effect of genetically predicted asthma on the risk of abnormal spermatozoa. Asthma, childhood-onset asthma (COA), and adult-onset asthma (AOA) (sample sizes ranging from 327,670 to 408,442) were included as the exposures. Genetic information for abnormal spermatozoa was obtained from a genome-wide association study (GWAS) comprising 209,921 participants. In univariable MR (UVMR) analysis, the inverse variance weighted (IVW) method was conducted as the primary method, with the MR Egger and weighted median used as supplementary methods for causal inference. Sensitivity analyses, including the Cochran Q test, Egger intercept test, MR-PRESSO, and leave-one-out analysis, were performed to verify the robustness of the MR results. Multivariable MR (MVMR) was conducted to evaluate the direct causal effects of asthma on abnormal spermatozoa risk. Results UVMR detected causal associations between genetically predicted asthma and an increased risk of abnormal spermatozoa (OR: 1.270, 95% CI: 1.045-1.545, p = 0.017). Moreover, we found that AOA (OR: 1.46, 95% CI: 1.051, 2.018, p = 0.024) has positive causal effects on the risk of abnormal spermatozoa rather than COA (p = 0.558). Sensitivity analysis found little evidence of bias in the current study (p > 0.05). MVMR further confirmed that asthma directly affected the risk of abnormal spermatozoa. Conclusion Our MR study suggested that genetically predicted asthma could be associated with an increased risk of abnormal spermatozoa, and similar results were obtained in AOA. Further studies are warranted to explain the underlying mechanisms of this association and may provide new avenues for prevention and treatment.
Collapse
Affiliation(s)
| | | | | | | | - Yaxuan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
24
|
Zhou Y, Yin X, Wang C, Yu D. Gene association analysis to determine the causal relationship between immune-mediated inflammatory diseases and frozen shoulder. Medicine (Baltimore) 2024; 103:e38055. [PMID: 38728465 PMCID: PMC11081594 DOI: 10.1097/md.0000000000038055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/05/2024] [Indexed: 05/12/2024] Open
Abstract
Multiple studies have indicated a potential correlation between immune-mediated inflammatory diseases (IMIDs) and Frozen shoulder (FS). To explore the genetic causal relationship between IMIDs and FS using 2-sample Mendelian randomization (MR) analysis. Genome-wide association study (GWAS) summary data for FS were obtained from Green's study, while data for 10 IMIDs were sourced from the FinnGen Consortium. The MR analysis was performed using inverse variance weighting, MR Egger, and weighted median methods. IVW, as the primary MR analysis technique, was complemented with other sensitivity analyses to validate the robustness of the results. Additionally, reverse MR analysis was further conducted to investigate the presence of reverse causal relationships. In the forward MR analysis, genetically determined 4 IMIDs are causally associated with FS: rheumatoid arthritis (odds ratio [OR] (95% confidence interval [95% CI]) = 1.05 [1.02-1.09], P < .01); type 1 diabetes (OR [95% CI] = 1.06 [1.03-1.09], P < .01); hypothyroidism (OR [95% CI] = 1.07 [1.01-1.14], P = .02); and Celiac disease (OR [95% CI] = 1.02 [1.01-1.04], P = .01). However, no causal relationship was found between 6 IMIDs (autoimmune hyperthyroidism, Crohn disease, ulcerative colitis, psoriasis, sicca syndrome and systemic lupus erythematosus) and FS. Sensitivity analyses did not detect any heterogeneity or horizontal pleiotropy. In the reverse MR analysis, no causal relationship was observed between FS and IMIDs. In conclusion, this MR study suggests a potential causal relationship between rheumatoid arthritis, type 1 diabetes, hypothyroidism, and Celiac disease in the onset and development of FS. Nevertheless, more basic and clinical research will be needed in the future to support our findings.
Collapse
Affiliation(s)
| | - Xiuping Yin
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | | | - Donglin Yu
- Binzhou Medical University, Yantai, China
| |
Collapse
|
25
|
Zhang M, Qiu J, Wang R. Mendelian randomization study on the causal effect of herpes simplex virus infection on idiopathic pulmonary fibrosis. Expert Rev Respir Med 2024; 18:341-347. [PMID: 38878268 DOI: 10.1080/17476348.2024.2369253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/13/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND Previous observational studies have shown that past infection of herpes simplex virus (HSV) is associated with idiopathic pulmonary fibrosis (IPF). The present study aims to identify the causal link between HSV infection (exposure factor) and IPF (outcome factor). RESEARCH DESIGN AND METHODS To date, the largest publicly available genome-wide association study (GWAS) for HSV infection (1,595 cases and 211,856 controls from Finnish ancestry) and for IPF (1,028 cases and 196,986 controls from Finnish ancestry) were used to perform this two-sample Mendelian randomization (MR) study. RESULTS We found no significant pleiotropy or heterogeneity of all selected nine HSV infection-associated genetic instrumental variants (IVs) in IPF GWAS dataset. Interestingly, we found that as HSV infection genetically increased, IPF risk increased based on an inverse-variance weighted (IVW) analysis (odds ratio [OR] = 1.280, 95% confidence interval [CI]: 1.048-1.563; p = 0.015) and weighted median (OR = 1.321, 95% CI: 1.032-1.692; p = 0.027). CONCLUSIONS Our analysis suggests a causal effect of genetically increased HSV infection on IPF risk. Thus, HSV infection may be a potential risk factor for IPF.
Collapse
Affiliation(s)
- Min Zhang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Jinming Qiu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Renxi Wang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
- Laboratory for Clinical Medicine, Capital Medical University, Beijing, China
| |
Collapse
|
26
|
Paschos NK. Editorial Commentary: Personalized Anterior Cruciate Ligament Reconstruction and Rehabilitation Mitigate Postoperative Arthrofibrosis: Prevention Is the Best Approach. Arthroscopy 2024; 40:1700-1702. [PMID: 38244022 DOI: 10.1016/j.arthro.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024]
Abstract
Arthrofibrosis after anterior cruciate ligament reconstruction can become a major complication requiring surgical intervention. The reported incidence approximates 8% but varies widely (2%-35%) and, as not all patients require surgery, may be underreported. Several risk factors are involved. Female sex, older age, surgery within the first month after injury, and meniscus repair are consistently associated with increased risk. Other factors include graft size and type, concomitant procedures, use of anticoagulants, and genetic factors. By identifying risk factors, we can modify our surgical technique and rehabilitation to meet each patient's needs with fewer complications.
Collapse
|
27
|
Xu Y, Gao R, Zhang M, Zeng Q, Zhou S, Zhu G, Su W, Wang R. Mendelian randomization study on causal association of FAM210B with drug-induced lupus. Clin Rheumatol 2024; 43:1513-1520. [PMID: 38436771 DOI: 10.1007/s10067-024-06903-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
OBJECTIVE Due to the complexity of drug-induced lupus (DIL) pathogenesis, more susceptibility factors need to be discovered. FAM210B is a new mitochondrial protein whose function has not been fully elucidated. This study will explore whether there is a correlation between FAM210B and the risk of DIL. METHODS At first, we extracted three FAM210B genetic variants from the GTEx database (n = 948), and extracted their corresponding genome-wide association study (GWAS) summary statistics from DIL (101 DIL cases and 218691 controls). Then, we performed a Mendelian randomization (MR) study to evaluate the causal association of the expression of FAM210B with DIL using inverse-variance weighted (IVW), the weighted median, MR-Egger, and MR-PRESSO test. RESULTS We successfully extracted three FAM210B single-nucleotide polymorphisms (SNPs) (rs116032784, rs34361943 and rs33923703) from the GTEx_Analysis_v8_eQTL data that can reduce FAM210B expression. The results of the MR analysis showed that genetically reduced expression of FAM210B was significantly associated with increased risk of DIL in European ancestry based on the IVW method (β = 1.037, p = 0.001, odds ratio [OR] = 2.821, 95% confidence interval [CI]:1.495-5.322). CONCLUSION MR analysis showed a causal relationship between FAM210B expression and the risk of DIL disease. Our results suggested that FAM210B may be a marker that can mark susceptibility of DIL in the future. It provides evidence for the study of DIL, but its specific mechanism of action in DIL needs to be further studied. Key Points •This is the first MR analysis to examine the association between FAM210B and DIL. •The findings of this study suggested that reduced FAM210B expression is associated with the increased risk of DIL. •FAM210B may be a marker that can mark susceptibility of DIL in the future.
Collapse
Affiliation(s)
- Yaqi Xu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China.
| | - Ran Gao
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China
| | - Min Zhang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China
| | - Qi Zeng
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China
| | - Shan Zhou
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China
| | - Gaizhi Zhu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China
| | - Wenting Su
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China
| | - Renxi Wang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China
| |
Collapse
|
28
|
Senkin S, Moody S, Díaz-Gay M, Abedi-Ardekani B, Cattiaux T, Ferreiro-Iglesias A, Wang J, Fitzgerald S, Kazachkova M, Vangara R, Le AP, Bergstrom EN, Khandekar A, Otlu B, Cheema S, Latimer C, Thomas E, Atkins JR, Smith-Byrne K, Cortez Cardoso Penha R, Carreira C, Chopard P, Gaborieau V, Keski-Rahkonen P, Jones D, Teague JW, Ferlicot S, Asgari M, Sangkhathat S, Attawettayanon W, Świątkowska B, Jarmalaite S, Sabaliauskaite R, Shibata T, Fukagawa A, Mates D, Jinga V, Rascu S, Mijuskovic M, Savic S, Milosavljevic S, Bartlett JMS, Albert M, Phouthavongsy L, Ashton-Prolla P, Botton MR, Silva Neto B, Bezerra SM, Curado MP, Zequi SDC, Reis RM, Faria EF, de Menezes NS, Ferrari RS, Banks RE, Vasudev NS, Zaridze D, Mukeriya A, Shangina O, Matveev V, Foretova L, Navratilova M, Holcatova I, Hornakova A, Janout V, Purdue MP, Rothman N, Chanock SJ, Ueland PM, Johansson M, McKay J, Scelo G, Chanudet E, Humphreys L, de Carvalho AC, Perdomo S, Alexandrov LB, Stratton MR, Brennan P. Geographic variation of mutagenic exposures in kidney cancer genomes. Nature 2024; 629:910-918. [PMID: 38693263 PMCID: PMC11111402 DOI: 10.1038/s41586-024-07368-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to cancer burden1. In clear cell renal cell carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do not explain the geographical variation in its incidence2. Underlying causes can be inferred by sequencing the genomes of cancers from populations with different incidence rates and detecting differences in patterns of somatic mutations. Here we sequenced 962 clear cell renal cell carcinomas from 11 countries with varying incidence. The somatic mutation profiles differed between countries. In Romania, Serbia and Thailand, mutational signatures characteristic of aristolochic acid compounds were present in most cases, but these were rare elsewhere. In Japan, a mutational signature of unknown cause was found in more than 70% of cases but in less than 2% elsewhere. A further mutational signature of unknown cause was ubiquitous but exhibited higher mutation loads in countries with higher incidence rates of kidney cancer. Known signatures of tobacco smoking correlated with tobacco consumption, but no signature was associated with obesity or hypertension, suggesting that non-mutagenic mechanisms of action underlie these risk factors. The results of this study indicate the existence of multiple, geographically variable, mutagenic exposures that potentially affect tens of millions of people and illustrate the opportunities for new insights into cancer causation through large-scale global cancer genomics.
Collapse
Affiliation(s)
- Sergey Senkin
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Thomas Cattiaux
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aida Ferreiro-Iglesias
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Stephen Fitzgerald
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Mariya Kazachkova
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Anh Phuong Le
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Saamin Cheema
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Emily Thomas
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Joshua Ronald Atkins
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, The Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Christine Carreira
- Evidence Synthesis and Classification Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Priscilia Chopard
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Valérie Gaborieau
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Pekka Keski-Rahkonen
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Jon W Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Sophie Ferlicot
- Service d'Anatomie Pathologique, Assistance Publique-Hôpitaux de Paris, Univeristé Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Mojgan Asgari
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Surasak Sangkhathat
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Worapat Attawettayanon
- Division of Urology, Department of Surgery, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Beata Świątkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Łódź, Poland
| | - Sonata Jarmalaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
- Department of Botany and Genetics, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Rasa Sabaliauskaite
- Laboratory of Genetic Diagnostic, National Cancer Institute, Vilnius, Lithuania
| | - Tatsuhiro Shibata
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
| | - Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Dana Mates
- Occupational Health and Toxicology Department, National Center for Environmental Risk Monitoring, National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Stefan Rascu
- Urology Department, Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Mirjana Mijuskovic
- Clinic of Nephrology, Faculty of Medicine, Military Medical Academy, Belgrade, Serbia
| | - Slavisa Savic
- Department of Urology, University Hospital Dr D. Misovic Clinical Center, Belgrade, Serbia
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - John M S Bartlett
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Monique Albert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Larry Phouthavongsy
- Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Patricia Ashton-Prolla
- Experimental Research Center, Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mariana R Botton
- Transplant Immunology and Personalized Medicine Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Brasil Silva Neto
- Service of Urology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Post-Graduate Program in Medicine: Surgical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Maria Paula Curado
- Department of Epidemiology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Stênio de Cássio Zequi
- Department of Urology, A. C. Camargo Cancer Center, São Paulo, Brazil
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, A.C. Camargo Cancer Center, São Paulo, Brazil
- Latin American Renal Cancer Group (LARCG), São Paulo, Brazil
- Department of Surgery, Division of Urology, Sao Paulo Federal University (UNIFESP), São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Minho University, Braga, Portugal
| | - Eliney Ferreira Faria
- Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
- Department of Urology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Rosamonde E Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Naveen S Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - David Zaridze
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Anush Mukeriya
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Oxana Shangina
- Department of Clinical Epidemiology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Vsevolod Matveev
- Department of Urology, N. N. Blokhin National Medical Research Centre of Oncology, Moscow, Russia
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Anna Hornakova
- Institute of Hygiene and Epidemiology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ghislaine Scelo
- Observational and Pragmatic Research Institute Pte Ltd, Singapore, Singapore
| | - Estelle Chanudet
- Department of Pathology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Ana Carolina de Carvalho
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Cambridge, UK
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France.
| |
Collapse
|
29
|
Wang X, Lu J, Han M, Wang Z, Zhang H, Liu Y, Zhou P, Fu J, Xie Y. Genome-wide expression quantitative trait locus analysis reveals silk-preferential gene regulatory network in maize. PHYSIOLOGIA PLANTARUM 2024; 176:e14386. [PMID: 38887947 DOI: 10.1111/ppl.14386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Silk of maize (Zea mays L.) contains diverse metabolites with complicated structures and functions, making it a great challenge to explore the mechanisms of metabolic regulation. Genome-wide identification of silk-preferential genes and investigation of their expression regulation provide an opportunity to reveal the regulatory networks of metabolism. Here, we applied the expression quantitative trait locus (eQTL) mapping on a maize natural population to explore the regulation of gene expression in unpollinated silk of maize. We obtained 3,985 silk-preferential genes that were specifically or preferentially expressed in silk using our population. Silk-preferential genes showed more obvious expression variations compared with broadly expressed genes that were ubiquitously expressed in most tissues. We found that trans-eQTL regulation played a more important role for silk-preferential genes compared to the broadly expressed genes. The relationship between 38 transcription factors and 85 target genes, including silk-preferential genes, were detected. Finally, we constructed a transcriptional regulatory network around the silk-preferential gene Bx10, which was proposed to be associated with response to abiotic stress and biotic stress. Taken together, this study deepened our understanding of transcriptome variation in maize silk and the expression regulation of silk-preferential genes, enhancing the investigation of regulatory networks on metabolic pathways.
Collapse
Affiliation(s)
- Xiaoli Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiawen Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingfang Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zheyuan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Peng Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxin Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
30
|
Li B, Li M, Qi X, Tong T, Zhang G. The causal associations of circulating lipids with Barrett's Esophagus and Esophageal Cancer: a bi-directional, two sample mendelian randomization analysis. Hum Genomics 2024; 18:37. [PMID: 38627859 PMCID: PMC11020202 DOI: 10.1186/s40246-024-00608-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE The causal associations of circulating lipids with Barrett's Esophagus (BE) and Esophageal Cancer (EC) has been a topic of debate. This study sought to elucidate the causality between circulating lipids and the risk of BE and EC. METHODS We conducted two-sample Mendelian randomization (MR) analyses using single nucleotide polymorphisms (SNPs) of circulating lipids (n = 94,595 - 431,167 individuals), BE (218,792 individuals), and EC (190,190 individuals) obtained from the publicly available IEU OpenGWAS database. The robustness and reliability of the results were ensured by employing inverse-variance weighted (IVW), weighted median, MR-Egger, and MR-PRESSO methods. The presence of horizontal pleiotropy, heterogeneities, and stability of instrumental variables were assessed through MR-Egger intercept test, Cochran's Q test, and leave-one-out sensitivity analysis. Additionally, bidirectional MR and multivariable MR (MVMR) were performed to explore reverse causality and adjust for known confounders, respectively. RESULTS None of the testing methods revealed statistically significant horizontal pleiotropy, directional pleiotropy, or heterogeneity. Univariate MR analyses using IVW indicated a robust causal relationship between increased triglycerides and BE (odds ratio [OR] = 1.79, p-value = 0.009), while no significant association with EC was observed. Inverse MR analysis indicated no evidence of reverse causality in the aforementioned outcomes. In MVMR analyses, elevated triglycerides (TRG) were significantly and positively associated with BE risk (OR = 1.79, p-value = 0.041). CONCLUSION This MR study suggested that genetically increased triglycerides were closely related to an elevated risk of BE, potentially serving as a biomarker for the diagnosis of BE in the future.
Collapse
Affiliation(s)
- Baofeng Li
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Meng Li
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Xiao Qi
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ti Tong
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun, Jilin, 130021, China.
| | - Guangxin Zhang
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun, Jilin, 130021, China.
| |
Collapse
|
31
|
Gao J, Yang Y, Xiang X, Zheng H, Yi X, Wang F, Liang Z, Chen D, Shi W, Wang L, Wu D, Feng S, Huang Q, Li X, Shu W, Chen R, Zhong N, Wang Z. Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease. Respir Res 2024; 25:165. [PMID: 38622589 DOI: 10.1186/s12931-024-02805-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10-5), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10-8). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.
Collapse
Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Yuqiong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xiaopeng Xiang
- The Hong Kong Polytechnic University, Hong Kong, Hung Hom Kowloon, China
| | - Huimin Zheng
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Fengyan Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhenyu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Dandan Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Weijuan Shi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Lingwei Wang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Di Wu
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengchuan Feng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Qiaoyun Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xueping Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China.
| | - Rongchang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
| | - Zhang Wang
- Institute of Ecological Sciences, Biomedical Research Center, School of Life Sciences, State Key Laboratory of Respiratory Disease, South China Normal University, Guangzhou, Guangdong Province, China.
| |
Collapse
|
32
|
Zhang Z, Zhang J, Jiao H, Tian W, Zhai X. Genetically predicted dietary macronutrient intakes and atrial fibrillation risk: a Mendelian randomization study. Eur J Med Res 2024; 29:227. [PMID: 38609963 PMCID: PMC11010414 DOI: 10.1186/s40001-024-01781-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/10/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND AND AIM Previous observational investigations have indicated a potential association between relative dietary macronutrient intakes and atrial fibrillation and flutter (AF) risk. In this study, we employed Mendelian Randomization (MR) to evaluate the presence of causality and to elucidate the specific causal relationship. METHODS We employed six, five, and three single nucleotide polymorphisms (SNPs) as instrumental variables for relative carbohydrate, protein, and fat intake, identified from a genome-wide association study that included 268,922 individuals of European descent. Furthermore, we acquired summary statistics for genome-wide association studies on AF from the FinnGen consortium, which involved 22,068 cases and 116,926 controls. To evaluate the causal estimates, we utilized the random effect inverse variance weighted method (IVW) and several other MR methods, including MR-Egger, weighted median, and MR-PRESSO, to confirm the robustness of our findings. RESULTS Our analysis indicates a convincing causal relationship between genetically predicted relative carbohydrate and protein intake and reduced AF risk. Inverse variance weighted analysis results for carbohydrates (OR = 0.29; 95% CI (0.14, 0.59); P < 0.001) and protein (OR = 0.47; 95% CI (0.26, 0.85); P = 0.01) support this association. Our MR analysis did not identify a significant causal relationship between relative fat intake and AF risk. CONCLUSION Our study provides evidence supporting a causal relationship between higher relative protein and carbohydrate intake and a lower risk of atrial fibrillation (AF).
Collapse
Affiliation(s)
- Zhuoya Zhang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiale Zhang
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Haoyang Jiao
- Institute of Documentation, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Tian
- Gaoyang County Hospital, Baoding, 071599, Hebei Province, China.
| | - Xu Zhai
- Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
| |
Collapse
|
33
|
Zhang W, Zhu J, Wu X, Feng T, Liao W, Li X, Chen J, Zhang L, Xiao C, Cui H, Yang C, Yan P, Wang Y, Tang M, Chen L, Liu Y, Zou Y, Wu X, Zhang L, Yang C, Yao Y, Li J, Liu Z, Jiang X, Zhang B. Phenotypic and genetic effect of carotid intima-media thickness on the risk of stroke. Hum Genet 2024:10.1007/s00439-024-02666-1. [PMID: 38578439 DOI: 10.1007/s00439-024-02666-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
While carotid intima-media thickness (cIMT) as a noninvasive surrogate measure of atherosclerosis is widely considered a risk factor for stroke, the intrinsic link underlying cIMT and stroke has not been fully understood. We aimed to evaluate the clinical value of cIMT in stroke through the investigation of phenotypic and genetic relationships between cIMT and stroke. We evaluated phenotypic associations using observational data from UK Biobank (N = 21,526). We then investigated genetic relationships leveraging genomic data conducted in predominantly European ancestry for cIMT (N = 45,185) and any stroke (AS, Ncase/Ncontrol=40,585/406,111). Observational analyses suggested an increased hazard of stroke per one standard deviation increase in cIMT (cIMTmax-AS: hazard ratio (HR) = 1.39, 95%CI = 1.09-1.79; cIMTmean-AS: HR = 1.39, 95%CI = 1.09-1.78; cIMTmin-AS: HR = 1.32, 95%CI = 1.04-1.68). A positive global genetic correlation was observed (cIMTmax-AS: [Formula: see text]=0.23, P=9.44 × 10-5; cIMTmean-AS: [Formula: see text]=0.21, P=3.00 × 10-4; cIMTmin-AS: [Formula: see text]=0.16, P=6.30 × 10-3). This was further substantiated by five shared independent loci and 15 shared expression-trait associations. Mendelian randomization analyses suggested no causal effect of cIMT on stroke (cIMTmax-AS: odds ratio (OR)=1.12, 95%CI=0.97-1.28; cIMTmean-AS: OR=1.09, 95%CI=0.93-1.26; cIMTmin-AS: OR=1.03, 95%CI = 0.90-1.17). A putative association was observed for genetically predicted stroke on cIMT (AS-cIMTmax: beta=0.07, 95%CI = 0.01-0.13; AS-cIMTmean: beta=0.08, 95%CI = 0.01-0.15; AS-cIMTmin: beta = 0.08, 95%CI = 0.01-0.16) in the reverse direction MR, which attenuated to non-significant in sensitivity analysis. Our work does not find evidence supporting causal associations between cIMT and stroke. The pronounced cIMT-stroke association is intrinsic, and mostly attributed to shared genetic components. The clinical value of cIMT as a surrogate marker for stroke risk in the general population is likely limited.
Collapse
Affiliation(s)
- Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Jingwei Zhu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Xuan Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Tianle Feng
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Wei Liao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Xuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Jianci Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Chenghan Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Ling Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Yuqin Yao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
| | - Zhenmi Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China School of Public Health and West China Fourth Hospital, West China- PUMC C. C. Chen Institute of Health, Sichuan University, No. 16, Section 3, South Renmin Road, Wuhou District, Chengdu, 610041, China.
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
- Department of Clinical Neuroscience, Karolinskaa Institutet, Stockholm, Sweden.
| | - Ben Zhang
- Hainan General Hospital and Hainan Affiliated Hospital, Hainan Medical University, Haikou, China; West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
| |
Collapse
|
34
|
Li J, Gao X, Sun X, Li H, Wei J, Lv L, Zhu L. Investigating the causal role of the gut microbiota in esophageal cancer and its subtypes: a two-sample Mendelian randomization study. BMC Cancer 2024; 24:416. [PMID: 38575885 PMCID: PMC10996172 DOI: 10.1186/s12885-024-12205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/29/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Through research on the gut microbiota (GM), increasing evidence has indicated that the GM is associated with esophageal cancer (ESCA). However, the specific cause-and-effect relationship remains unclear. In this study, Mendelian randomization (MR) analysis was applied to investigate the causal relationship between the GM and ESCA, including its subtypes. METHODS We collected information on 211 GMs and acquired data on ESCA and its subtypes through genome-wide association studies (GWASs). The causal relationship was primarily assessed using the inverse variance weighted (IVW) method. Additionally, we applied the weighted median estimator (WME) method, MR-Egger method, weighted mode, and simple mode to provide further assistance. Subsequent to these analyses, sensitivity analysis was conducted using the MR-Egger intercept test, MR-PRESSO global test, and leave-one-out method. RESULT Following our assessment using five methods and sensitivity analysis, we identified seven GMs with potential causal relationships with ESCA and its subtypes. At the genus level, Veillonella and Coprobacter were positively correlated with ESCA, whereas Prevotella9, Eubacterium oxidoreducens group, and Turicibacter were negatively correlated with ESCA. In the case of esophageal adenocarcinoma (EAC), Flavonifractor exhibited a positive correlation, while Actinomyces exhibited a negative correlation. CONCLUSION Our study revealed the potential causal relationship between GM and ESCA and its subtypes, offering novel insights for the advancement of ESCA diagnosis and treatment.
Collapse
Affiliation(s)
- Jia Li
- Thoracic Surgery Department, Jinan Central Hospital, Shandong University, Jinan, 250000, China
| | - Xuedi Gao
- Thoracic Surgery Department, Jinan Mingshui Eye Hospital, Jinan, 250000, China
| | - Xiaoming Sun
- Thoracic Surgery Department, Jinan Central Hospital, Jinan, 250000, China
| | - Hao Li
- Thoracic Surgery Department, Jinan Central Hospital, Shandong First Medical University, Jinan, 250000, China
| | - Jiaheng Wei
- Thoracic Surgery Department, Weifang Medical University, Weifang, 261000, China
| | - Lin Lv
- Thoracic Surgery Department, Jinan Central Hospital, Shandong University, Jinan, 250000, China
| | - Liangming Zhu
- Thoracic Surgery Department, Jinan Central Hospital, Shandong University, Jinan, 250000, China.
| |
Collapse
|
35
|
Tong F, Wang Y, Gao Q, Zhao Y, Zhang X, Li B, Wang X. The epidemiology of pregnancy loss: global burden, variable risk factors, and predictions. Hum Reprod 2024; 39:834-848. [PMID: 38308812 DOI: 10.1093/humrep/deae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/15/2023] [Indexed: 02/05/2024] Open
Abstract
STUDY QUESTION Is the incidence of pregnancy loss correlated with various geographic, socio-demographic, and age stratifications at the societal and national levels, and what are the risk factors associated with pregnancy loss at the individual level? SUMMARY ANSWER The epidemiological trends and disease burden of pregnancy loss were correlated with various geographic, socio-demographic, and age stratifications, and we identified that poor health condition, smoking, sedentary behaviour, lower educational level, and lower maternal birth weight may significantly increase the risk of pregnancy loss. WHAT IS KNOWN ALREADY Several studies have used national, regional, or single-centre data to describe trends in the burden of pregnancy loss, and previous observational studies have identified some variable factors possibly associated with pregnancy loss. However, a comprehensive analysis of global trends and predictions of pregnancy loss are lacking, and the conclusions have been inconsistent. STUDY DESIGN, SIZE, DURATION We have utilized the data from Global Burden of Disease (GBD) 2019 to provide an overview of the trends in pregnancy loss in 204 countries and regions worldwide from 1990 to 2019, and have made a forecast for the next 10 years. Moreover, we applied a variety of statistical genetics methods to analyse 34 239 pregnancy loss and 89 340 non-pregnancy loss cases from the FinnGen consortium to comprehensively assess the bidirectional causality of variable factors with pregnancy loss from an individual perspective. PARTICIPANTS/MATERIALS, SETTING, METHODS We analysed trends in the incidence, disability-adjusted life years (DALYs), and maternal mortality of pregnancy loss at global, regional, national, socio-demographic index (SDI), and age levels. The autoregressive integrated moving average (ARIMA) model was used to predict trends by 2030. Finally, we used two-sample Mendelian randomization (MR) and multivariate MR (MVMR) analyses to explore the relationship between the pregnancy loss and variables closely related to physical condition, physical activity, lifestyle, sleep conditions, basic conditions. MAIN RESULTS AND THE ROLE OF CHANCE In 2019, there were approximately 42.39 million cases of pregnancy loss worldwide. Globally, the incidence, DALYs, and mortality of pregnancy loss showed a decreasing trend between 1990 and 2019, although the number was increasing in some countries. The age-standardized incidence, DALYs, and mortality rate were negatively correlated with SDI level and show a further decline by 2030. Based on MR analyses, we confirmed that genetically predicted overall health rating (inverse-variance weighted (IVW) odds ratio (OR), 1.68; 95% CI, 1.34-2.13; P = 5.10 × 10-6), smoking initiation (IVW OR, 1.26; 95% CI, 1.16-1.38; P = 1.90 × 10-9), sedentary behaviour (IVW OR, 1.56; 95% CI, 1.20-2.01; P = 2.76 × 10-5), educational level (IVW OR, 0.64; 95% CI, 0.55-0.73; P = 6.56 × 10-10), and maternal birth weight (IVW OR, 0.70; 95% CI, 0.58-0.85; P = 2.98 × 10-4) were significantly related to the risk of pregnancy loss, whereas body mass index (IVW OR, 1.10; 95% CI, 1.03-1.17; P = 5.31 × 10-3), alcohol consumption (IVW OR, 1.74; 95% CI, 1.03-2.95; P = 0.04), insomnia (IVW OR, 1.66; 95% CI, 1.14-2.42; P = 7.00 × 10-3), and moderate-to-vigorous physical activity (IVW OR, 0.59; 95% CI, 0.37-0.95; P = 2.85 × 10-2) were suggestively associated with the risk of pregnancy loss. These results were supported by sensitivity and directional analyses. LIMITATIONS, REASONS FOR CAUTION Despite efforts to standardize GBD data from all over the world, uncertainties in data quality control regarding ascertainment of pregnancy loss, medical care accessibility, cultural differences, and socioeconomic status still exist. Furthermore, the population in the MRstudy was limited to Europeans, which means that the results may not be extrapolated to people of other origins. WIDER IMPLICATIONS OF THE FINDINGS Our study provides for the first time an overview of the epidemiological trends and disease burden of pregnancy loss related with SDI, region, country, and age, and predicts changes in future trends up to 2030. In addition, findings support that genetic susceptibility, smoking, health condition, and sedentary behaviour may be powerful indicators of an increased risk of pregnancy loss. These results would be beneficial for policy makers of different countries and regions to improve prevention implementation. STUDY FUNDING/COMPETING INTERESTS This work was supported by grants 2021JH2/10300093, from the Science and Technology Projects of Liaoning Province, China. All authors declare no conflicts of interest. TRIAL REGISTRATION NUMBER N/A.
Collapse
Affiliation(s)
- Fei Tong
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yue Wang
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qianqian Gao
- Department of Obstetrics, Weifang People's Hospital, Weifang, Shandong, China
| | - Yan Zhao
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xu Zhang
- Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, China
| | - Baoxuan Li
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoyan Wang
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| |
Collapse
|
36
|
Liu X, Yuan J, Wang X, Tang M, Meng X, Zhang L, Wang S, Zhang H. Association between rheumatoid arthritis and autoimmune thyroid disease: evidence from complementary genetic methods. Endocrine 2024; 84:171-178. [PMID: 37884826 DOI: 10.1007/s12020-023-03571-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
OBJECTIVES To assess the causal association of Rheumatoid Arthritis (RA) with Autoimmune thyroid disease (AITD). METHOD Complementary genetic approaches, including genetic correlation, Mendelian randomization (MR) and colocalization analysis, were conducted to assess the potential causal association between RA and AITD using summary statistics from large-scale genome-wide association studies (GWASs). Various sensitivity analyses had been conducted to assess the robustness and the consistency of the findings. RESULTS The linkage disequilibrium score regression revealed a shared genetic structure between RA and AITD, with the significant genetic correlation between RA and autoimmune hyperthyroidism and autoimmune hypothyroidism estimated to be 0.3945 (P = 2.83 × 10-6) and 0.2771 (P = 1.04 × 10-6) respectively. The results of MR analysis showed that RA had a positive causal relationship with autoimmune hypothyroidism and autoimmune hyperthyroidism. The odds ratio (OR) were 1.29 (95% CI, 1.17-1.42; P = 1.08 × 10-7) and 1.47 (95% CI, 1.25-1.72; P = 1.85 × 10-6), respectively. In reverse MR analysis, autoimmune hypothyroidism had a positive causal relationship with RA, OR was 1.51 (95% CI, 1.37-1.66; P = 1.10 × 10-16); autoimmune hyperthyroidism had no causal relationship with RA relationship (P = 0.22). Similar results were found using different MR methods. In addition, colocalization analysis suggested that shared causal variants existed between RA and AITD. CONCLUSIONS Our study suggested a potentially causal effect of genetically predicted RA on autoimmune hyperthyroidism and a bidirectional causal relationship between RA and autoimmune hypothyroidism was also observed with complementary genetic approaches, which supports the importance and necessity of thyroid function screening and monitoring in RA patient management in clinical practice.
Collapse
Affiliation(s)
- Xue Liu
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Jie Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China
| | - Xinhui Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Mulin Tang
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Xue Meng
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Li Zhang
- Department of Vascular Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Shukang Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
| | - Haiqing Zhang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, 250021, China.
- Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, 250021, China.
| |
Collapse
|
37
|
Campbell KA, Fu M, MacDonald E, Zawistowski M, Bakulski KM, Ware EB. Relationship between alcohol consumption and dementia with Mendelian randomization approaches among older adults in the United States. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2024; 16:e12598. [PMID: 38903149 PMCID: PMC11187745 DOI: 10.1002/dad2.12598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 06/22/2024]
Abstract
INTRODUCTION In observational studies, the association between alcohol consumption and dementia is mixed. METHODS We performed two-sample Mendelian randomization (MR) using summary statistics from genome-wide association studies of weekly alcohol consumption and late-onset Alzheimer's disease and one-sample MR in the Health and Retirement Study (HRS), wave 2012. Inverse variance weighted two-stage regression provided odds ratios of association between alcohol exposure and dementia or cognitively impaired, non-dementia relative to cognitively normal. RESULTS Alcohol consumption was not associated with late-onset Alzheimer's disease using two-sample MR (odds ratio [OR] = 1.15, 95% confidence interval [CI]: [0.78, 1.72]). In HRS, doubling weekly alcohol consumption was not associated with dementia (African ancestries, n = 1,322, OR = 1.00, 95% CI [0.45, 2.25]; European ancestries, n = 7,160, OR = 1.37, 95% CI [0.53, 3.51]) or cognitively impaired, non-dementia (African ancestries, n = 1,322, OR = 1.17, 95% CI [0.69, 1.98]; European ancestries, n = 7,160, OR = 0.75, 95% CI [0.47, 1.22]). DISCUSSION Alcohol consumption was not associated with cognitively impaired, non-dementia or dementia status. Highlights Cross-sectionally in a large, diverse sample, alcohol appears protective for dementia.We apply two- and one-sample Mendelian randomization to test inferred causality.Mendelian randomization approaches show no association with alcohol and dementia.We conclude that alcohol consumption should not be considered protective.
Collapse
Affiliation(s)
- Kyle A. Campbell
- Department of EpidemiologyUniversity of Michigan School of Public HealthAnn ArborMichiganUSA
| | - Mingzhou Fu
- Department of EpidemiologyUniversity of Michigan School of Public HealthAnn ArborMichiganUSA
| | - Elizabeth MacDonald
- Department of EpidemiologyUniversity of Michigan School of Public HealthAnn ArborMichiganUSA
| | - Matthew Zawistowski
- Department of BiostatisticsUniversity of Michigan School of Public HealthAnn ArborMichiganUSA
| | - Kelly M. Bakulski
- Department of EpidemiologyUniversity of Michigan School of Public HealthAnn ArborMichiganUSA
| | - Erin B. Ware
- Institute for Social ResearchUniversity of MichiganAnn ArborMichiganUSA
| |
Collapse
|
38
|
Yan Z, Xu Y, Li K, Liu L. Association between genetically proxied lipid-lowering drug targets, lipid traits, and amyotrophic lateral sclerosis: a mendelian randomization study. Acta Neurol Belg 2024; 124:485-494. [PMID: 37889424 DOI: 10.1007/s13760-023-02393-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND The use of circulating lipid traits as biomarkers to predict the risk of amyotrophic lateral sclerosis (ALS) is currently controversial, and the evidence-based medical evidence for the use of lipid-lowering agents, especially statins, on ALS risk remains insufficient. Our aim was to apply a Mendelian randomization (MR) approach to assess the causal impact of lipid-lowering agents and circulating lipid traits on ALS risk. MATERIALS AND METHODS Our study included primary and secondary analyses, in which the risk associations of lipid-lowering gene inhibitors, lipid traits, and ALS were assessed by the inverse variance weighting method as the primary approach. The robustness of the results was assessed using LDSC assessment, conventional MR sensitivity analysis, and used Mediating MR to explore potential mechanisms of occurrence. In the secondary analysis, the association of lipid-lowering genes with ALS was validated using the Summary data-based Mendelian Randomization (SMR) method. RESULTS Our results showed strong evidence between genetic proxies for Apolipoprotein B (ApoB) inhibitor (OR = 0.76, 95% CI = 0.68 - 0.86; P = 5.58 × 10-6) and reduced risk of ALS. Additionally, 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) inhibitor (OR = 1.06, 95% CI = 0. 85-1.33) was not found to increase ALS risk. SMR results suggested that ApoB expression was associated with increased ALS risk, and colocalization analysis did not support a significant common genetic variation between ApoB and ALS. Mediator MR analysis suggested a possible mediating role for interleukin-6 and low-density lipoprotein cholesterol (LDL-C). While elevated LDL-C was significantly associated with increased risk of ALS among lipid traits, total cholesterol (TC) and ApoB were weakly associated with ALS. LDSC results suggested a potential genetic correlation between these lipid traits and ALS. CONCLUSIONS Using ApoB inhibitor can lower the risk of ALS, statins do not trigger ALS, and LDL-C, TC, and ApoB levels can predict the risk of ALS.
Collapse
Affiliation(s)
- Zhaoqi Yan
- Graduate School, Jiangxi University of Traditional Chinese Medicine, Yangming Road, Nanchang, Jiangxi, China
| | - Yifeng Xu
- Graduate School, Jiangxi University of Traditional Chinese Medicine, Yangming Road, Nanchang, Jiangxi, China
| | - Keke Li
- Graduate School, Jiangxi University of Traditional Chinese Medicine, Yangming Road, Nanchang, Jiangxi, China
| | - Liangji Liu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, 445 Bayi Dadao, Nanchang, Jiangxi, China.
| |
Collapse
|
39
|
Pott J, Kheirkhah A, Gadin JR, Kleber ME, Delgado GE, Kirsten H, Forer L, Hauck SM, Burkhardt R, Scharnagl H, Loeffler M, März W, Thiery J, Gieger C, Peters A, Silveira A, Hooft FV, Kronenberg F, Scholz M. Sex and statin-related genetic associations at the PCSK9 gene locus: results of genome-wide association meta-analysis. Biol Sex Differ 2024; 15:26. [PMID: 38532495 DOI: 10.1186/s13293-024-00602-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a key player of lipid metabolism with higher plasma levels in women throughout their life. Statin treatment affects PCSK9 levels also showing evidence of sex-differential effects. It remains unclear whether these differences can be explained by genetics. METHODS We performed genome-wide association meta-analyses (GWAS) of PCSK9 levels stratified for sex and statin treatment in six independent studies of Europeans (8936 women/11,080 men respectively 14,825 statin-free/5191 statin-treated individuals). Loci associated in one of the strata were tested for statin- and sex-interactions considering all independent signals per locus. Independent variants at the PCSK9 gene locus were then used in a stratified Mendelian Randomization analysis (cis-MR) of PCSK9 effects on low-density lipoprotein cholesterol (LDL-C) levels to detect differences of causal effects between the subgroups. RESULTS We identified 11 loci associated with PCSK9 in at least one stratified subgroup (p < 1.0 × 10-6), including the PCSK9 gene locus and five other lipid loci: APOB, TM6SF2, FADS1/FADS2, JMJD1C, and HP/HPR. The interaction analysis revealed eight loci with sex- and/or statin-interactions. At the PCSK9 gene locus, there were four independent signals, one with a significant sex-interaction showing stronger effects in men (rs693668). Regarding statin treatment, there were two significant interactions in PCSK9 missense mutations: rs11591147 had stronger effects in statin-free individuals, and rs11583680 had stronger effects in statin-treated individuals. Besides replicating known loci, we detected two novel genome-wide significant associations: one for statin-treated individuals at 6q11.1 (within KHDRBS2) and one for males at 12q24.22 (near KSR2/NOS1), both with significant interactions. In the MR of PCSK9 on LDL-C, we observed significant causal estimates within all subgroups, but significantly stronger causal effects in statin-free subjects compared to statin-treated individuals. CONCLUSIONS We performed the first double-stratified GWAS of PCSK9 levels and identified multiple biologically plausible loci with genetic interaction effects. Our results indicate that the observed sexual dimorphism of PCSK9 and its statin-related interactions have a genetic basis. Significant differences in the causal relationship between PCSK9 and LDL-C suggest sex-specific dosages of PCSK9 inhibitors.
Collapse
Affiliation(s)
- Janne Pott
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK.
| | - Azin Kheirkhah
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Jesper R Gadin
- Division of Cardiovascular Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Solna, Sweden
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ralph Burkhardt
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Hubert Scharnagl
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
- SYNLAB Academy, Synlab Holding Deutschland GmbH, Mannheim and Augsburg, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Faculty of Medicine, University of Kiel, Kiel, Germany
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Angela Silveira
- Division of Cardiovascular Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Solna, Sweden
| | - Ferdinand Van't Hooft
- Division of Cardiovascular Medicine, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Solna, Sweden
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.
| |
Collapse
|
40
|
Hirtz R, Grasemann C, Hölling H, von Holt BH, Albers N, Hinney A, Hebebrand J, Peters T. No relationship between male pubertal timing and depression - new insights from epidemiology and Mendelian randomization. Psychol Med 2024:1-10. [PMID: 38515277 DOI: 10.1017/s0033291724000060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
BACKGROUND In males, the relationship between pubertal timing and depression is understudied and less consistent than in females, likely for reasons of unmeasured confounding. To clarify this relationship, a combined epidemiological and genetic approach was chosen to exploit the methodological advantages of both approaches. METHODS Data from 2026 males from a nationwide, representative study were used to investigate the non-/linear relationship between pubertal timing defined by the age at voice break and depression, considering a multitude of potential confounders and their interactions with pubertal timing. This analysis was complemented by Mendelian randomization (MR), which is robust to inferential problems inherent to epidemiological studies. We used 71 single nucleotide polymorphisms related to pubertal timing in males as instrumental variable to clarify its causal relationship with depression based on data from 807 553 individuals (246 363 cases and 561 190 controls) by univariable and multivariable MR, including BMI as pleiotropic phenotype. RESULTS Univariable MR indicated a causal effect of pubertal timing on depression risk (inverse-variance weighted: OR 0.93, 95%-CI [0.87-0.99)], p = 0.03). However, this was not confirmed by multivariable MR (inverse-variance weighted: OR 0.95, 95%-CI [0.88-1.02)], p = 0.13), consistent with the epidemiological approach (OR 1.01, 95%-CI [0.81-1.26], p = 0.93). Instead, the multivariable MR study indicated a causal relationship of BMI with depression by two of three methods. CONCLUSIONS Pubertal timing is not related to MDD risk in males.
Collapse
Affiliation(s)
- Raphael Hirtz
- Department of Pediatrics, Division of Rare Diseases, and CeSER, Ruhr-University Bochum, Alexandrinenstr. 5, 44791 Bochum, Germany
- Division of Pediatric Endocrinology and Diabetology, Department of Pediatrics II, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 40211 Essen, Germany
- Helios University Medical Centre Wuppertal - Children's Hospital, Witten/Herdecke University, Wuppertal, Germany
| | - Corinna Grasemann
- Division of Pediatric Endocrinology and Diabetology, Department of Pediatrics II, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 40211 Essen, Germany
| | - Heike Hölling
- Department of Epidemiology and Health Monitoring, Robert Koch Institute, Berlin, Germany
| | - Björn-Hergen von Holt
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, 23562 Lübeck, Germany
| | - Nicola Albers
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 174, 45147 Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 174, 45147 Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 174, 45147 Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Triinu Peters
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Virchowstr. 174, 45147 Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
41
|
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] [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
|
42
|
Shi K, Yu Y, Li Z, Hou M, Li X. Causal relationship between dietary salt intake and dementia risk: Mendelian randomization study. GENES & NUTRITION 2024; 19:6. [PMID: 38491466 PMCID: PMC10943813 DOI: 10.1186/s12263-024-00741-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/10/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVE Observational research has indicated a potential link between dietary salt intake and susceptibility to dementia. However, it is important to note that these types of studies are prone to the issues of reverse causation and residual confounding. Therefore, we conducted a two-sample Mendelian randomization (MR) study to explore the causality. METHOD To explore the causal relationship between them, this Mendelian randomization (MR) study incorporated summary statistics of dietary salt intake and dementia. We estimated the causality between salt intake and the risk of overall dementia and various subtypes of dementia, including Alzheimer's disease (AD), Vascular dementia (VaD), and Lewy body dementia (LBD). The inverse variance-weighted (IVW) method was the major MR analysis. To conduct sensitivity analyses, we employed various MR methods, the pleiotropy residual sum and outlier (MR-PRESSO) method, and the leave-one-out approach. The MR-Egger intercept and Cochran's Q test were conducted to test pleiotropy and heterogeneity respectively. RESULTS A suggestive association was observed for genetically predicted higher dietary salt intake and increased risk of overall dementia in the European ancestry [odds ratio (OR): 1.542; 95% confidence interval (95% CI): 1.095-2.169; P = 0.013]. The causal relationship between dietary salt intake and overall dementia is robust with respect to the choice of statistical methods and is validated through extensive sensitivity analyses that guard against various model assumption violations. Meanwhile, no clear heterogeneity or pleiotropy was identified. However, we failed to detect a causal effect of dietary salt intake on the risk of various dementia subtypes. CONCLUSION The results of this research present strong evidence that established a significant association between dietary salt intake and the likelihood of developing dementia. These findings reinforce the notion that the amount of dietary salt intake plays a crucial role in determining the risk of acquiring this cognitive condition. By establishing a definitive correlation, this study highlights the importance of reducing salt consumption as a preventive measure against dementia.
Collapse
Affiliation(s)
- Ke Shi
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Tongji Shanxi Hospital, Shanxi Academy of Medical Sciences, Taiyuan, 030032, China
| | - Yongbo Yu
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Tongji Shanxi Hospital, Shanxi Academy of Medical Sciences, Taiyuan, 030032, China
| | - Zhaolin Li
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Tongji Shanxi Hospital, Shanxi Academy of Medical Sciences, Taiyuan, 030032, China
| | - Miaomiao Hou
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Tongji Shanxi Hospital, Shanxi Academy of Medical Sciences, Taiyuan, 030032, China
| | - Xinyi Li
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Tongji Shanxi Hospital, Shanxi Academy of Medical Sciences, Taiyuan, 030032, China.
| |
Collapse
|
43
|
Chen X, Wang S, Shen W. The causal relationship between severe mental illness and risk of lung carcinoma. Medicine (Baltimore) 2024; 103:e37355. [PMID: 38489734 PMCID: PMC10939700 DOI: 10.1097/md.0000000000037355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 03/17/2024] Open
Abstract
Observational studies have suggested a link between severe mental illness (SMI) and risk of lung carcinoma (LC); however, causality has not been established. In this study, we conducted a two-sample, two-step Mendelian randomization (MR) investigation to uncover the etiological influence of SMI on LC risk and quantify the mediating effects of known modifiable risk factors. We obtained summary-level datasets for schizophrenia, major depressive disorder (MDD), and bipolar disorder (BD) from the Psychiatric Genomics Consortium (PGC). Data on single nucleotide polymorphisms (SNPs) associated with lung carcinoma (LC) were sourced from a recent large meta-analysis by McKay et al. We employed two-sample MR and two-step MR utilizing the inverse variance weighted method for causal estimation. Sensitivity tests were conducted to validate causal relationships. In two-sample MR, we identified schizophrenia as a risk factor for LC (OR = 1.06, 95% CI 1.02-1.11, P = 3.48E-03), while MDD (OR = 1.18, 95% CI 0.98-1.42, P = .07) and BD (OR = 1.07, 95% CI 0.99-1.15, P = .09) showed no significant association with LC. In the two-step MR, smoking accounted for 24.66% of the schizophrenia-LC risk association, and alcohol consumption explained 7.59% of the effect. Schizophrenia is a risk factor for lung carcinoma, and smoking and alcohol consumption are the mediating factors in this causal relationship. LC screening should be emphasized in individuals with schizophrenia, particularly in those who smoke and consume alcohol regularly.
Collapse
Affiliation(s)
- Xiaohan Chen
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Shudan Wang
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| | - Weiyu Shen
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
| |
Collapse
|
44
|
Aalborg T, Sverrisdóttir E, Kristensen HT, Nielsen KL. The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato. FRONTIERS IN PLANT SCIENCE 2024; 15:1340189. [PMID: 38525152 PMCID: PMC10957621 DOI: 10.3389/fpls.2024.1340189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait. The impact of such redundant "diluted" predictors on the statistical models underpinning genome-wide association studies (GWAS) and genomic prediction has scarcely been evaluated despite the potential impact on model accuracy and performance. We evaluated the impact of marker location, marker type, and marker density on the genomic prediction and GWAS of five key performance traits in tetraploid potato (chipping quality, dry matter content, length/width ratio, senescence, and yield). A 762-offspring panel of a diallel cross of 18 elite cultivars was genotyped by sequencing, and markers were annotated according to a reference genome. Genomic prediction models (GBLUP) were trained on four marker subsets [non-synonymous (29,553 SNPs), synonymous (31,229), non-coding (32,388), and a combination], and robustness to marker reduction was investigated. Single-marker regression GWAS was performed for each trait and marker subset. The best cross-validated prediction correlation coefficients of 0.54, 0.75, 0.49, 0.35, and 0.28 were obtained for chipping quality, dry matter content, length/width ratio, senescence, and yield, respectively. The trait prediction abilities were similar across all marker types, with only non-synonymous variants improving yield predictive ability by 16%. Marker reduction response did not depend on marker type but rather on trait. Traits with high predictive abilities, e.g., dry matter content, reached a plateau using fewer markers than traits with intermediate-low correlations, such as yield. The predictions were unbiased across all traits, marker types, and all marker densities >100 SNPs. Our results suggest that using non-synonymous variants does not enhance the performance of genomic prediction of most traits. The major known QTLs were identified by GWAS and were reproducible across exonic and whole-genome variant sets for dry matter content, length/width ratio, and senescence. In contrast, minor QTL detection was marker type dependent.
Collapse
Affiliation(s)
- Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | | | | |
Collapse
|
45
|
Zhang W, Zhang L, Xiao C, Wu X, Cui H, Yang C, Yan P, Tang M, Wang Y, Chen L, Liu Y, Zou Y, Zhang L, Yang C, Yao Y, Li J, Liu Z, Jiang X, Zhang B. Bidirectional relationship between type 2 diabetes mellitus and coronary artery disease: Prospective cohort study and genetic analyses. Chin Med J (Engl) 2024; 137:577-587. [PMID: 38062574 DOI: 10.1097/cm9.0000000000002894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND While type 2 diabetes mellitus (T2DM) is considered a putative causal risk factor for coronary artery disease (CAD), the intrinsic link underlying T2DM and CAD is not fully understood. We aimed to highlight the importance of integrated care targeting both diseases by investigating the phenotypic and genetic relationships between T2DM and CAD. METHODS We evaluated phenotypic associations using data from the United Kingdom Biobank ( N = 472,050). We investigated genetic relationships by leveraging genomic data conducted in European ancestry for T2DM, with and without adjustment for body mass index (BMI) (T2DM: Ncase / Ncontrol = 74,124/824,006; T2DM adjusted for BMI [T2DM adj BMI]: Ncase / Ncontrol = 50,409/523,897) and for CAD ( Ncase / Ncontrol = 181,522/984,168). We performed additional analyses using genomic data conducted in multiancestry individuals for T2DM ( Ncase / Ncontrol = 180,834/1,159,055). RESULTS Observational analysis suggested a bidirectional relationship between T2DM and CAD (T2DM→CAD: hazard ratio [HR] = 2.12, 95% confidence interval [CI]: 2.01-2.24; CAD→T2DM: HR = 1.72, 95% CI: 1.63-1.81). A positive overall genetic correlation between T2DM and CAD was observed ( rg = 0.39, P = 1.43 × 10 -75 ), which was largely independent of BMI (T2DM adj BMI-CAD: rg = 0.31, P = 1.20 × 10 -36 ). This was corroborated by six local signals, among which 9p21.3 showed the strongest genetic correlation. Cross-trait meta-analysis replicated 101 previously reported loci and discovered six novel pleiotropic loci. Mendelian randomization analysis supported a bidirectional causal relationship (T2DM→CAD: odds ratio [OR] = 1.13, 95% CI: 1.11-1.16; CAD→T2DM: OR = 1.12, 95% CI: 1.07-1.18), which was confirmed in multiancestry individuals (T2DM→CAD: OR = 1.13, 95% CI: 1.10-1.16; CAD→T2DM: OR = 1.08, 95% CI: 1.04-1.13). This bidirectional relationship was significantly mediated by systolic blood pressure and intake of 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors, with mediation proportions of 54.1% (95% CI: 24.9-83.4%) and 90.4% (95% CI: 29.3-151.5%), respectively. CONCLUSION Our observational and genetic analyses demonstrated an intrinsic bidirectional relationship between T2DM and CAD and clarified the biological mechanisms underlying this relationship.
Collapse
Affiliation(s)
- Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenghan Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ling Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuqin Yao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhenmi Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, West China-Peking Union Medical College C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| |
Collapse
|
46
|
Liu X, Yuan J, Liu S, Wang X, Tang M, Meng X, Li Y, Chai Y, Wang Y, Tian G, Liu X, Zhou H, Kou C, Zhang L, Yuan Z, Zhang H. The causal relationship between autoimmune thyroid disorders and telomere length: A Mendelian randomization and colocalization study. Clin Endocrinol (Oxf) 2024; 100:294-303. [PMID: 38214116 DOI: 10.1111/cen.15004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 10/20/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024]
Abstract
This study aimed to evaluate whether there is a causal relationship between autoimmune thyroid disorders (AITDs) and telomere length (TL) in the European population and whether there is reverse causality. In this study, Mendelian randomization (MR) and colocalization analysis were conducted to assess the potential causal relationship between AITDs and TL using summary statistics from large-scale genome-wide association studies, followed by analysis of the relationship between TL and thyroid stimulating hormone and free thyroxine (FT4) to help interpret the findings. The inverse variance weighted (IVW) method was used to estimate the causal estimates. The weighted median, MR-Egger and leave-one-out methods were used as sensitivity analyses. The IVW method results showed a significant causal relationship between autoimmune hyperthyroidism and TL (β = -1.93 × 10-2 ; p = 4.54 × 10-5 ). There was no causal relationship between autoimmune hypothyroidism and TL (β = -3.99 × 10-3 ; p = 0.324). The results of the reverse MR analysis showed that genetically TL had a significant causal relationship on autoimmune hyperthyroidism (IVW: odds ratio (OR) = 0.49; p = 2.83 × 10-4 ) and autoimmune hypothyroidism (IVW: OR = 0.86; p = 7.46 × 10-3 ). Both horizontal pleiotropy and heterogeneity tests indicated the validity of our bidirectional MR study. Finally, colocalization analysis suggested that there were shared causal variants between autoimmune hyperthyroidism and TL, further highlighting the robustness of the results. In conclusion, autoimmune hyperthyroidism may accelerate telomere attrition, and telomere attrition is a causal factor for AITDs.
Collapse
Affiliation(s)
- Xue Liu
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Jie Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shuai Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xinhui Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Mulin Tang
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xue Meng
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yuchen Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Yuwei Chai
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Yuyao Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Guoyu Tian
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Xueying Liu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huizhi Zhou
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Chunjia Kou
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Li Zhang
- Department of Vascular Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Haiqing Zhang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, China
- Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, China
| |
Collapse
|
47
|
Mao Z, Gao ZX, Ji T, Huan S, Yin GP, Chen L. Bidirectional two-sample mendelian randomization analysis identifies causal associations of MRI-based cortical thickness and surface area relation to NAFLD. Lipids Health Dis 2024; 23:58. [PMID: 38395962 PMCID: PMC10885469 DOI: 10.1186/s12944-024-02043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) patients have exhibited extra-hepatic neurological changes, but the causes and mechanisms remain unclear. This study investigates the causal effect of NAFLD on cortical structure through bidirectional two-sample Mendelian randomization analysis. METHODS Genetic data from 778,614 European individuals across four NAFLD studies were used to determine genetically predicted NAFLD. Abdominal MRI scans from 32,860 UK Biobank participants were utilized to evaluate genetically predicted liver fat and volume. Data from the ENIGMA Consortium, comprising 51,665 patients, were used to evaluate the associations between genetic susceptibility, NAFLD risk, liver fat, liver volume, and alterations in cortical thickness (TH) and surface area (SA). Inverse-variance weighted (IVW) estimation, Cochran Q, and MR-Egger were employed to assess heterogeneity and pleiotropy. RESULTS Overall, NAFLD did not significantly affect cortical SA or TH. However, potential associations were noted under global weighting, relating heightened NAFLD risk to reduced parahippocampal SA and decreased cortical TH in the caudal middle frontal, cuneus, lingual, and parstriangularis regions. Liver fat and volume also influenced the cortical structure of certain regions, although no Bonferroni-adjusted p-values reached significance. Two-step MR analysis revealed that liver fat, AST, and LDL levels mediated the impact of NAFLD on cortical structure. Multivariable MR analysis suggested that the impact of NAFLD on the cortical TH of lingual and parstriangularis was independent of BMI, obesity, hyperlipidemia, and diabetes. CONCLUSION This study provides evidence that NAFLD causally influences the cortical structure of the brain, suggesting the existence of a liver-brain axis in the development of NAFLD.
Collapse
Affiliation(s)
- Zun Mao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Zhi-Xiang Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Tong Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Sheng Huan
- Department of Anesthesiology and Perioperative Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, P. R. China
| | - Guo-Ping Yin
- Department of Anesthesiology, Nanjing Second Hospital, Nanjing, 210000, P. R. China.
| | - Long Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, P. R. China.
| |
Collapse
|
48
|
Yan Z, Xu Y, Li K, Liu L. Association between high-density lipoprotein cholesterol and type 2 diabetes mellitus: dual evidence from NHANES database and Mendelian randomization analysis. Front Endocrinol (Lausanne) 2024; 15:1272314. [PMID: 38455653 PMCID: PMC10917910 DOI: 10.3389/fendo.2024.1272314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Background Low levels of high-density lipoprotein cholesterol (HDL-C) are commonly seen in patients with type 2 diabetes mellitus (T2DM). However, it is unclear whether there is an independent or causal link between HDL-C levels and T2DM. This study aims to address this gap by using the The National Health and Nutrition Examination Survey (NHANES) database and Mendelian randomization (MR) analysis. Materials and methods Data from the NHANES survey (2007-2018) with 9,420 participants were analyzed using specialized software. Logistic regression models and restricted cubic splines (RCS) were used to assess the relationship between HDL-C and T2DM incidence, while considering covariates. Genetic variants associated with HDL-C and T2DM were obtained from genome-wide association studies (GWAS), and Mendelian randomization (MR) was used to evaluate the causal relationship between HDL-C and T2DM. Various tests were conducted to assess pleiotropy and outliers. Results In the NHANES study, all groups, except the lowest quartile (Q1: 0.28-1.09 mmol/L], showed a significant association between HDL-C levels and reduced T2DM risk (all P < 0.001). After adjusting for covariates, the Q2 [odds ratio (OR) = 0.67, 95% confidence interval (CI): (0.57, 0.79)], Q3 [OR = 0.51, 95% CI: (0.40, 0.65)], and Q4 [OR = 0.29, 95% CI: (0.23, 0.36)] groups exhibited average reductions in T2DM risk of 23%, 49%, and 71%, respectively. In the sensitivity analysis incorporating other lipid levels, the Q4 group still demonstrates a 57% reduction in the risk of T2DM. The impact of HDL-C levels on T2DM varied with age (P for interaction = 0.006). RCS analysis showed a nonlinear decreasing trend in T2DM risk with increasing HDL-C levels (P = 0.003). In the MR analysis, HDL-C levels were also associated with reduced T2DM risk (OR = 0.69, 95% CI = 0.52-0.82; P = 1.41 × 10-13), and there was no evidence of pleiotropy or outliers. Conclusion This study provides evidence supporting a causal relationship between higher HDL-C levels and reduced T2DM risk. Further research is needed to explore interventions targeting HDL-C levels for reducing T2DM risk.
Collapse
Affiliation(s)
- Zhaoqi Yan
- Jiangxi University of Traditional Chinese Medicine, Graduate School, Nanchang, Jiangxi, China
| | - Yifeng Xu
- Jiangxi University of Traditional Chinese Medicine, Graduate School, Nanchang, Jiangxi, China
| | - Keke Li
- Jiangxi University of Traditional Chinese Medicine, Graduate School, Nanchang, Jiangxi, China
| | - Liangji Liu
- Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Department of Respiratory and Critical Care Medicine, Nanchang, Jiangxi, China
| |
Collapse
|
49
|
Aierken A, Atabieke F, Aierken M, Li J, Xia Y, Aizezi Y, Li SX. No bidirectional relationship between inflammatory bowel disease and diverticular disease: a genetic correlation and Mendelian randomization study. Front Genet 2024; 15:1334473. [PMID: 38419785 PMCID: PMC10899511 DOI: 10.3389/fgene.2024.1334473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Background: Although previous studies found that inflammatory bowel disease (IBD) and diverticular disease (DD) usually co-exist clinically, studies examining the relationship are spare. Aim: Our study aspires to investigate the causal correlation between the IBD [including ulcerative colitis (UC) and Crohn's disease (CD)] and DD using the Mendelian randomization (MR) analysis. Methods: We conducted a two-sample bidirectional MR analysis using publicly available genome-wide association studies (GWAS) summary data. The single nucleotide polymorphism (SNP) data associated with DD and IBD were obtained from the Finnish Biobank and UK Biobank, respectively. Through secondary data analysis of all GWAS summary data, we systematically screened genetic instrumental variables. To address the impact of horizontal pleiotropy, several methods were employed, including the inverse variance-weighted method (IVW), maximum likelihood method, Egger regression method, weighted median method, and simple median method. These approaches aimed to detect and correct for the potential bias caused by horizontal pleiotropy. Results: Genetically predicted DD did not have a causal effect on IBD (OR 1.06, 95% CI 0.98-1.17, p = 0.15), and had no causal effect on UC (OR 1.10, 95% CI 0.94-1.20, p = 0.36) and CD (OR 1.03, 95% CI 0.92-1.16, p = 0.62) either. Furthermore, in the reverse MR analysis, we did not observe any significant causal effect of IBD on DD. Results of complementary methods showed consistent results with those of the IVW method. Conclusion: This study's findings do not provide evidence for a causal relationship between IBD and DD, which contradicts the majority of observational studies.
Collapse
Affiliation(s)
- Ailikamu Aierken
- Graduate School of Xinjiang Medical University, Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Falide Atabieke
- The Second Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Munire Aierken
- Department of Disinfection and Vector-Borne Pathogen Control, Urumqi City Center for Disease Prevention and Control, Urumqi, China
| | - Jian Li
- The Second Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yu Xia
- The Second Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yierzhati Aizezi
- Center of Critical Care Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shui-Xue Li
- Department of General Surgery, Children's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| |
Collapse
|
50
|
Wang M, Zhang Z, Daghlas I, Gill D, Liu D, Lian X. Adiposity and Functional Outcome After Ischemic Stroke: A Mendelian Randomization Study. Neurology 2024; 102:e208080. [PMID: 38181322 DOI: 10.1212/wnl.0000000000208080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/19/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND AND OBJECTIVES To investigate the causal relationships of abdominal adiposity (waist-to-hip ratio [WHR]) and overall adiposity (body mass index [BMI]) with functional outcome after ischemic stroke using Mendelian randomization. METHODS Genetic instruments for WHR and BMI were obtained from the largest available genome-wide association studies meta-analysis of the Genetic Investigation of ANthropometric Traits consortium and the UK Biobank (N max = 806,834). Functional outcome after ischemic stroke was assessed using the modified Rankin Scale (mRS) score at 3-month after stroke onset, with mRS >2 (mRS 3-6) defined as an unfavorable functional outcome. Corresponding genetic estimates for an unfavorable functional outcome were extracted from the Genetics of Ischemic Stroke Functional Outcome network (N = 6,021). We applied a random-effects inverse variance weighted method as our main analysis. RESULTS Genetically predicted higher WHR (per 0.09 ratio units) was associated with unfavorable functional outcome after ischemic stroke (mRS 3-6, OR = 1.48; 95% CI = 1.03-2.13; p = 0.033). The results remained directionally consistent in sensitivity analyses. Conversely, genetically predicted BMI (per 4.8 kg/m2) was not associated with unfavorable functional outcome after ischemic stroke (OR = 1.01; 95% CI = 0.75-1.36; p = 0.937). DISCUSSION This study provides genetic evidence supporting the hypothesis that abdominal adiposity has a detrimental effect on functional recovery after ischemic stroke.
Collapse
Affiliation(s)
- Mengmeng Wang
- From the Department of Neurology (M.W., X.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China; Department of Neurology (Z.Z.), Jinling Hospital, Medical School of Nanjing University, China; Department of Neurology (I.D.), University of California San Francisco; Department of Epidemiology and Biostatistics (D.G.), School of Public Health, St Mary's Hospital, Imperial College London, United Kingdom; and Department of Integrated Traditional Chinese and Western Medicine (D.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Zhizhong Zhang
- From the Department of Neurology (M.W., X.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China; Department of Neurology (Z.Z.), Jinling Hospital, Medical School of Nanjing University, China; Department of Neurology (I.D.), University of California San Francisco; Department of Epidemiology and Biostatistics (D.G.), School of Public Health, St Mary's Hospital, Imperial College London, United Kingdom; and Department of Integrated Traditional Chinese and Western Medicine (D.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Iyas Daghlas
- From the Department of Neurology (M.W., X.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China; Department of Neurology (Z.Z.), Jinling Hospital, Medical School of Nanjing University, China; Department of Neurology (I.D.), University of California San Francisco; Department of Epidemiology and Biostatistics (D.G.), School of Public Health, St Mary's Hospital, Imperial College London, United Kingdom; and Department of Integrated Traditional Chinese and Western Medicine (D.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Dipender Gill
- From the Department of Neurology (M.W., X.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China; Department of Neurology (Z.Z.), Jinling Hospital, Medical School of Nanjing University, China; Department of Neurology (I.D.), University of California San Francisco; Department of Epidemiology and Biostatistics (D.G.), School of Public Health, St Mary's Hospital, Imperial College London, United Kingdom; and Department of Integrated Traditional Chinese and Western Medicine (D.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Dandan Liu
- From the Department of Neurology (M.W., X.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China; Department of Neurology (Z.Z.), Jinling Hospital, Medical School of Nanjing University, China; Department of Neurology (I.D.), University of California San Francisco; Department of Epidemiology and Biostatistics (D.G.), School of Public Health, St Mary's Hospital, Imperial College London, United Kingdom; and Department of Integrated Traditional Chinese and Western Medicine (D.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xuegan Lian
- From the Department of Neurology (M.W., X.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China; Department of Neurology (Z.Z.), Jinling Hospital, Medical School of Nanjing University, China; Department of Neurology (I.D.), University of California San Francisco; Department of Epidemiology and Biostatistics (D.G.), School of Public Health, St Mary's Hospital, Imperial College London, United Kingdom; and Department of Integrated Traditional Chinese and Western Medicine (D.L.), The Third Affiliated Hospital of Soochow University, Changzhou, China
| |
Collapse
|