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Jiang Y, Chen P, Zhao Y, Zhang Y. Association of Cadherin-Related Family Member 1 with Traumatic Brain Injury. Cell Mol Neurobiol 2024; 44:41. [PMID: 38656449 DOI: 10.1007/s10571-024-01476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The cadherin family plays a pivotal role in orchestrating synapse formation in the central nervous system. Cadherin-related family member 1 (CDHR1) is a photoreceptor-specific calmodulin belonging to the expansive cadherin superfamily. However, its role in traumatic brain injury (TBI) remains largely unknown. CDHR1 expression across various brain tissue sites was analyzed using the GSE104687 dataset. Employing a summary-data-based Mendelian Randomization (SMR) approach, integrated analyses were performed by amalgamating genome-wide association study abstracts from TBI with public data on expressed quantitative trait loci and DNA methylation QTL from both blood and diverse brain tissues. CDHR1 expression and localization in different brain tissues were meticulously delineated using western blotting, immunohistochemistry, and enzyme-linked immunosorbent assay. CDHR1 expression was consistently elevated in the TBI group compared to that in the sham group across multiple tissues. The inflammatory response emerged as a crucial biological mechanism, and pro-inflammatory and anti-inflammatory factors were not expressed in either group. Integrated SMR analyses encompassing both blood and brain tissues substantiated the heightened CDHR1 expression profiles, with methylation modifications emerging as potential contributing factors for increased TBI risk. This was corroborated by western blotting and immunohistochemistry, confirming augmented CDHR1 expression following TBI. This multi-omics-based genetic association study highlights the elevated TBI risk associated with CDHR1 expression coupled with putative methylation modifications. These findings provide compelling evidence for future targeted investigations and offer promising avenues for developing interventional therapies for TBI.
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Affiliation(s)
- Yong'An Jiang
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
- Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Peng Chen
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
- Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - YangYang Zhao
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
- Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yan Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
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Qin S, Jiang Y, Ou Y, Zhan Y, Ji L, Xu P, Shao X, Chen H, Chen T, Cheng Y. Mendelian randomization of circulating proteome identifies IFN-γ as a druggable target in aplastic anemia. Ann Hematol 2024:10.1007/s00277-024-05746-4. [PMID: 38644415 DOI: 10.1007/s00277-024-05746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Aplastic anemia (AA) is a kind of bone marrow failure (BMF) characterized by pancytopenia with hypoplasia/aplasia of bone marrow. Immunosuppressive therapy and bone marrow transplantation are effective methods to treat severe aplastic anemia. However, the efficacy is limited by complications and the availability of suitable donors. This study aimed to determine whether any circulating druggable protein levels may have causal effects on AA and provide potential novel drug targets for AA. METHODS Genetic variants strongly associated with circulating druggable protein levels to perform Mendelian randomization (MR) analyses were used. The effect of these druggable protein levels on AA risk was measured using the summary statistics from a large-scale proteomic genome-wide association study (GWAS) and FinnGen database ( https://www.finngen.fi/en/access_results ). Multivariable MR analyses were performed to statistically adjust for potential confounders, including platelet counts, reticulocyte counts, neutrophil counts, and proportions of hematopoietic stem cells. RESULTS The data showed that higher level of circulating IFN-γ levels was causally associated with AA susceptibility. The causal effects of circulating IFN-γ levels on the AA were broadly consistent, when adjusted for platelet counts, reticulocyte counts, neutrophil counts and proportions of hematopoietic stem cells. CONCLUSIONS High levels of circulating IFN-γ levels might increase the risk of AA and might provide a potential novel target for AA.
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Affiliation(s)
- Shanshan Qin
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yingxin Jiang
- Centenary Institute, The University of Sydney, Sydney, NSW, 2050, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yang Ou
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yanxia Zhan
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lili Ji
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Pengcheng Xu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xia Shao
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Hao Chen
- Department of Thoracic Surgery, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200237, China
| | - Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Yunfeng Cheng
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China.
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Wan X, Yu H, Yang M, Hou W, Xie J, Xu K, Ma Y, Ma R, Wang F, Xu P. Study on the causal relationship between educational attainment and delirium: A two-sample Mendelian randomization study. Heliyon 2024; 10:e28697. [PMID: 38571646 PMCID: PMC10988048 DOI: 10.1016/j.heliyon.2024.e28697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 01/26/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
This study aimed to investigate whether there is a causal relationship between educational attainment and delirium at the genetic level using the Mendelian randomization method, and provide new evidence for studies in this field. We found a causal relationship between educational attainment and delirium at the genetic level after excluding confounders using Mendelian randomization. The inverse variance weighting method of random effects was the main analysis method. The weighted median and Mendelian Randomization-Egger methods, as well as simple, and weighted modes were used as supplementary analysis methods. Additionally, horizontal pleiotropy tests were conducted, including the Mendelian Randomization-Egger intercept test and Mendelian Randomization Pleiotropy RESidual Sum and Outlier. Cochran's Q statistic was used to assess the size of heterogeneity. We retrieved all second single nucleotide polymorphism features and performed multivariate Mendelian randomization to adjust for the effect of potential confounders on our results. The inverse variance weighting suggested a negative correlation between genetically predicted educational attainment and delirium (0.67[0.49-0.92], p = 0.013); Mendelian Randomization Pleiotropy RESidual Sum and Outlier (0.67[0.49-0.92], p = 0.013) and multivariate Mendelian randomization (0.52[0.33-0.82], p = 0.005) results were generally consistent with the inverse variance weighting method. The Mendelian Randomization-Egger, simple, and weighted mode results were consistent with the inverse variance weighting results. Our results were not affected by pleiotropy or heterogeneity (p > 0.05, for both pleiotropy and heterogeneity). In addition, the "leave-one-out" analysis showed that the results of our Mendelian randomization analysis were not influenced by individual single nucleotide polymorphisms. Studies have found a causal relationship between educational attainment and delirium at the genetic level; higher educational attainment may be a protective factor against delirium. Clinically, more attention should be paid to patients at a high risk of delirium with low educational attainment.
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Affiliation(s)
| | | | - Mingyi Yang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Weikun Hou
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Jiale Xie
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Yujie Ma
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Rui Ma
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Fan Wang
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, China
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Nelson PT, Fardo DW, Wu X, Aung KZ, Cykowski MD, Katsumata Y. Limbic-predominant age-related TDP-43 encephalopathy (LATE-NC): Co-pathologies and genetic risk factors provide clues about pathogenesis. J Neuropathol Exp Neurol 2024:nlae032. [PMID: 38613823 DOI: 10.1093/jnen/nlae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2024] Open
Abstract
Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is detectable at autopsy in more than one-third of people beyond age 85 years and is robustly associated with dementia independent of other pathologies. Although LATE-NC has a large impact on public health, there remain uncertainties about the underlying biologic mechanisms. Here, we review the literature from human studies that may shed light on pathogenetic mechanisms. It is increasingly clear that certain combinations of pathologic changes tend to coexist in aging brains. Although "pure" LATE-NC is not rare, LATE-NC often coexists in the same brains with Alzheimer disease neuropathologic change, brain arteriolosclerosis, hippocampal sclerosis of aging, and/or age-related tau astrogliopathy (ARTAG). The patterns of pathologic comorbidities provide circumstantial evidence of mechanistic interactions ("synergies") between the pathologies, and also suggest common upstream influences. As to primary mediators of vulnerability to neuropathologic changes, genetics may play key roles. Genes associated with LATE-NC include TMEM106B, GRN, APOE, SORL1, ABCC9, and others. Although the anatomic distribution of TDP-43 pathology defines the condition, important cofactors for LATE-NC may include Tau pathology, endolysosomal pathways, and blood-brain barrier dysfunction. A review of the human phenomenology offers insights into disease-driving mechanisms, and may provide clues for diagnostic and therapeutic targets.
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Affiliation(s)
- Peter T Nelson
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky, USA
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
| | - David W Fardo
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
| | - Xian Wu
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
| | - Khine Zin Aung
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
| | - Matthew D Cykowski
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Yuriko Katsumata
- Department of Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, USA
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
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Guo M, Deng L, Gu J, Miao J, Yin J, Li Y, Fang Y, Huang B, Sun Z, Qi F, Dong W, Lu Z, Li S, Hu J, Zhang X, Ren L. Genome-wide association study and development of molecular markers for yield and quality traits in peanut (Arachis hypogaea L.). BMC Plant Biol 2024; 24:244. [PMID: 38575936 PMCID: PMC10996145 DOI: 10.1186/s12870-024-04937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND This study aims to decipher the genetic basis governing yield components and quality attributes of peanuts, a critical aspect for advancing molecular breeding techniques. Integrating genotype re-sequencing and phenotypic evaluations of seven yield components and two grain quality traits across four distinct environments allowed for the execution of a genome-wide association study (GWAS). RESULTS The nine phenotypic traits were all continuous and followed a normal distribution. The broad heritability ranged from 88.09 to 98.08%, and the genotype-environment interaction effects were all significant. There was a highly significant negative correlation between protein content (PC) and oil content (OC). The 10× genome re-sequencing of 199 peanut accessions yielded a total of 631,988 high-quality single nucleotide polymorphisms (SNPs), with 374 significant SNP loci identified in association with the nine traits of interest. Notably, 66 of these pertinent SNPs were detected in multiple environments, and 48 of them were linked to multiple traits of interest. Five loci situated on chromosome 16 (Chr16) exhibited pleiotropic effects on yield traits, accounting for 17.64-32.61% of the observed phenotypic variation. Two loci on Chr08 were found to be strongly associated with protein and oil contents, accounting for 12.86% and 14.06% of their respective phenotypic variations, respectively. Linkage disequilibrium (LD) block analysis of these seven loci unraveled five nonsynonymous variants, leading to the identification of one yield-related candidate gene and two quality-related candidate genes. The correlation between phenotypic variation and SNP loci in these candidate genes was validated by Kompetitive allele-specific PCR (KASP) marker analysis. CONCLUSIONS Overall, molecular markers were developed for genetic loci associated with yield and quality traits through a GWAS investigation of 199 peanut accessions across four distinct environments. These molecular tools can aid in the development of desirable peanut germplasm with an equilibrium of yield and quality through marker-assisted breeding.
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Affiliation(s)
- Minjie Guo
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Li Deng
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianzhong Gu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Jianli Miao
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junhua Yin
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yang Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Yuanjin Fang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Bingyan Huang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Ziqi Sun
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Feiyan Qi
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhenhua Lu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Shaowei Li
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Junping Hu
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China
| | - Xinyou Zhang
- Shennong Laboratory, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Li Ren
- Peanut Institute, Kaifeng Academy of Agricultural and Forestry Sciences, Kaifeng, 475004, China.
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Tebeka S, Gloaguen E, Mullaert J, He Q, Boland A, Deleuze JF, Jamet C, Ramoz N, Dubertret C. Genome-wide association study of early-onset and late-onset postpartum depression: the IGEDEPP prospective study. Eur Psychiatry 2024:1-36. [PMID: 38555957 DOI: 10.1192/j.eurpsy.2024.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Affiliation(s)
- Sarah Tebeka
- Université Paris Cité, INSERM U1266, F-75014 Paris, France
- Department of Psychiatry, AP-HP, Louis Mourier Hospital, F-92700 Colombes, France
| | - Emilie Gloaguen
- Department of Epidemiology, Biostatistics and Clinical Research, AP-HP, Hôpital Bichat, F-75018 Paris, France
| | - Jimmy Mullaert
- Department of Epidemiology, Biostatistics and Clinical Research, AP-HP, Hôpital Bichat, F-75018 Paris, France
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France
| | - Qin He
- Université Paris Cité, INSERM U1266, F-75014 Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-Francois Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Camille Jamet
- Université Paris Cité, INSERM U1266, F-75014 Paris, France
- Department of Psychiatry, AP-HP, Louis Mourier Hospital, F-92700 Colombes, France
| | - Nicolas Ramoz
- Université Paris Cité, INSERM U1266, F-75014 Paris, France
| | - Caroline Dubertret
- Université Paris Cité, INSERM U1266, F-75014 Paris, France
- Department of Psychiatry, AP-HP, Louis Mourier Hospital, F-92700 Colombes, France
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Holen B, Kutrolli G, Shadrin AA, Icick R, Hindley G, Rødevand L, O'Connell KS, Frei O, Parker N, Tesfaye M, Deak JD, Jahołkowski P, Dale AM, Djurovic S, Andreassen OA, Smeland OB. Genome-wide analyses reveal shared genetic architecture and novel risk loci between opioid use disorder and general cognitive ability. Drug Alcohol Depend 2024; 256:111058. [PMID: 38244365 DOI: 10.1016/j.drugalcdep.2023.111058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/09/2023] [Accepted: 12/03/2023] [Indexed: 01/22/2024]
Abstract
BACKGROUND Opioid use disorder (OUD), a serious health burden worldwide, is associated with lower cognitive function. Recent studies have demonstrated a negative genetic correlation between OUD and general cognitive ability (COG), indicating a shared genetic basis. However, the specific genetic variants involved, and the underlying molecular mechanisms remain poorly understood. Here, we aimed to quantify and identify the genetic basis underlying OUD and COG. METHODS We quantified the extent of genetic overlap between OUD and COG using a bivariate causal mixture model (MiXeR) and identified specific genetic loci applying conditional/conjunctional FDR. Finally, we investigated biological function and expression of implicated genes using available resources. RESULTS We estimated that ~94% of OUD variants (4.8k out of 5.1k variants) also influence COG. We identified three novel OUD risk loci and one locus shared between OUD and COG. Loci identified implicated biological substrates in the basal ganglia. CONCLUSION We provide new insights into the complex genetic risk architecture of OUD and its genetic relationship with COG.
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Affiliation(s)
- Børge Holen
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway.
| | - Gleda Kutrolli
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Alexey A Shadrin
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Romain Icick
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway; INSERM UMR-S1144, Université Paris Cité, F-75006, France
| | - Guy Hindley
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Linn Rødevand
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Kevin S O'Connell
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Oleksandr Frei
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Nadine Parker
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Markos Tesfaye
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway; NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Joseph D Deak
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Piotr Jahołkowski
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Anders M Dale
- Department of Radiology, University of California San Diego, La Jolla, CA 92093, USA; Multimodal Imaging Laboratory, University of California San Diego, La Jolla, CA 92093, USA; Department of Cognitive Science, University of California San Diego, La Jolla, CA, USA; Department of Psychiatry, University of California San Diego, La Jolla, CA, USA; Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole A Andreassen
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Olav B Smeland
- NORMENT, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway.
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Pena-Fernández N, Ocejo M, van der Graaf-van Bloois L, Lavín JL, Kortabarria N, Collantes-Fernández E, Hurtado A, Aduriz G. Comparative pangenomic analysis of Campylobacter fetus isolated from Spanish bulls and other mammalian species. Sci Rep 2024; 14:4347. [PMID: 38388650 PMCID: PMC10884003 DOI: 10.1038/s41598-024-54750-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/15/2024] [Indexed: 02/24/2024] Open
Abstract
Campylobacter fetus comprises two closely related mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv). The latter causes bovine genital campylobacteriosis, a sexually-transmitted disease endemic in Spain that results in significant economic losses in the cattle industry. Here, 33 C. fetus Spanish isolates were whole-genome sequenced and compared with 62 publicly available C. fetus genomes from other countries. Genome-based taxonomic identification revealed high concordance with in silico PCR, confirming Spanish isolates as Cff (n = 4), Cfv (n = 9) and Cfv biovar intermedius (Cfvi, n = 20). MLST analysis assigned the Spanish isolates to 6 STs, including three novel: ST-76 and ST-77 for Cfv and ST-78 for Cff. Core genome SNP phylogenetic analysis of the 95 genomes identified multiple clusters, revealing associations at subspecies and biovar level between genomes with the same ST and separating the Cfvi genomes from Spain and other countries. A genome-wide association study identified pqqL as a Cfv-specific gene and a potential candidate for more accurate identification methods. Functionality analysis revealed variations in the accessory genome of C. fetus subspecies and biovars that deserve further studies. These results provide valuable information about the regional variants of C. fetus present in Spain and the genetic diversity and predicted functionality of the different subspecies.
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Affiliation(s)
- Nerea Pena-Fernández
- SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Carretera de Oviedo, s/n, 33300, Villaviciosa, Spain
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Medelin Ocejo
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Linda van der Graaf-van Bloois
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jose Luís Lavín
- Department of Applied Mathematics, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Nekane Kortabarria
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Esther Collantes-Fernández
- Animal Health Department, Faculty of Veterinary Sciences, SALUVET, Complutense University of Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain
| | - Ana Hurtado
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain.
| | - Gorka Aduriz
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain.
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Sáez ME, García-Sánchez A, de Rojas I, Alarcón-Martín E, Martínez J, Cano A, García-González P, Puerta R, Olivé C, Capdevila M, García-Gutiérrez F, Castilla-Martí M, Castilla-Martí L, Espinosa A, Alegret M, Ricciardi M, Pytel V, Valero S, Tárraga L, Boada M, Ruiz A, Marquié M. Genome-wide association study and polygenic risk scores of retinal thickness across the cognitive continuum: data from the NORFACE cohort. Alzheimers Res Ther 2024; 16:38. [PMID: 38365752 PMCID: PMC10870444 DOI: 10.1186/s13195-024-01398-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND Several studies have reported a relationship between retinal thickness and dementia. Therefore, optical coherence tomography (OCT) has been proposed as an early diagnosis method for Alzheimer's disease (AD). In this study, we performed a genome-wide association study (GWAS) aimed at identifying genes associated with retinal nerve fiber layer (RNFL) and ganglion cell inner plexiform layer (GCIPL) thickness assessed by OCT and exploring the relationships between the spectrum of cognitive decline (including AD and non-AD cases) and retinal thickness. METHODS RNFL and GCIPL thickness at the macula were determined using two different OCT devices (Triton and Maestro). These determinations were tested for association with common single nucleotide polymorphism (SNPs) using adjusted linear regression models and combined using meta-analysis methods. Polygenic risk scores (PRSs) for retinal thickness and AD were generated. RESULTS Several genetic loci affecting retinal thickness were identified across the genome in accordance with previous reports. The genetic overlap between retinal thickness and dementia, however, was weak and limited to the GCIPL layer; only those observable with all-type dementia cases were considered. CONCLUSIONS Our study does not support the existence of a genetic link between dementia and retinal thickness.
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Grants
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
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Affiliation(s)
- María Eugenia Sáez
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Centro Andaluz de Estudios Bioinformáticos (CAEBI), Seville, Spain
| | - Ainhoa García-Sánchez
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Itziar de Rojas
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Emilio Alarcón-Martín
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Joan Martínez
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Amanda Cano
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo García-González
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Raquel Puerta
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Clàudia Olivé
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Maria Capdevila
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | | | - Miguel Castilla-Martí
- Clínica Oftalmológica Dr. Castilla, Barcelona, Spain
- Vista Alpina Eye Clinic, Visp, Switzerland
| | - Luis Castilla-Martí
- PhD Programme in Surgery and Morphological Sciences, Universitat Autònoma de Barcelona, Barcelona, Spain
- Hôpital ophtalmique Jules-Gonin, Fondation asiles des aveugles, University of Lausanne, Lausanne, Switzerland
| | - Ana Espinosa
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Alegret
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Mario Ricciardi
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Vanesa Pytel
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Sergi Valero
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Lluís Tárraga
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercè Boada
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín Ruiz
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain.
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
- Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, Texas, USA.
| | - Marta Marquié
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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10
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Dai Q, Guo Y, Dong X, Gao Y, Li S, Zhao J, Xu Y, Liu K. The role of leptin in ischemic stroke and its subtypes: A Mendelian randomization study. Nutr Metab Cardiovasc Dis 2024; 34:360-368. [PMID: 37949710 DOI: 10.1016/j.numecd.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND AND AIMS Observational studies have suggested a relationship between leptin and risk of stroke. However, evidence for the association remains inconsistent, and whether the association reflects a causal relationship remains to be established. To clarify this relationship, we adopted a two-sample Mendelian randomization (MR) analysis to investigate whether leptin plays a causal role in the risk of stroke and its subtypes. METHODS AND RESULTS Five independent single-nucleotide polymorphisms (SNPs) associated with the leptin level from genome-wide association studies (GWASs) of European individuals were selected. We performed an MR analysis using the inverse-variance-weighted (IVW) as primary method to examine the causal effects of leptin on ischemic stroke (IS). Moreover, MR-Egger intercept and Cochran's Q statistic were also performed to detect the pleiotropy or heterogeneity of our MR results. Genetically predicted circulating leptin level was not associated with ischemic stroke [odds ratio (OR): 1.48, 95% confidence interval (CI): 0.78-2.8, P = 0.22], large artery stroke (OR: 1.44, 95% CI: 0.39-5.25, P = 0.57), cardioembolic stroke (OR:1.33, 95% CI: 0.55-3.22, P = 0.52), and small vessel stroke (OR: 1.48, 95% CI: 0.39-5.63, P = 0.56) using the IVW method. Likewise, there is no convincing evidence for the associations between leptin levels and cardiovascular diseases (CVD) risk factors. CONCLUSIONS This study did not provide evidence that leptin levels are associated with increased risk of stroke and its subtypes.
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Affiliation(s)
- Qinqin Dai
- Nursing School of Zhengzhou University, Zhengzhou, Henan Province, China; The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yuanli Guo
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China; Nursing School of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiaofang Dong
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China; Nursing School of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yuan Gao
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China; Nursing School of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Shen Li
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Jiawei Zhao
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yuming Xu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Kai Liu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China; Nursing School of Zhengzhou University, Zhengzhou, Henan Province, China.
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11
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Chen Y, Wu X, Zhang Y, Chen J. Genetic causal association between frozen shoulder and carpal tunnel syndrome: a two-sample mendelian randomization. BMC Musculoskelet Disord 2024; 25:58. [PMID: 38216946 PMCID: PMC10790250 DOI: 10.1186/s12891-024-07186-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/09/2024] [Indexed: 01/14/2024] Open
Abstract
OBJECTIVE Observational studies have suggested an association between frozen shoulder (FS) and carpal tunnel syndrome (CTS). However, due to challenges in establishing a temporal sequence, the causal relationship between these two conditions remains elusive. This study, based on aggregated data from large-scale population-wide genome-wide association studies (GWAS), investigates the genetic causality between FS and CTS. METHODS Initially, a series of quality control measures were employed to select single nucleotide polymorphisms (SNPs) closely associated with the exposure factors. Two-sample Mendelian randomization (MR) was utilized to examine the genetic causality between FS and CTS, employing methods including Inverse-Variance Weighted (IVW), MR-Egger, Weighted Median, Simple Mode, and Weighted Mode approaches. Subsequently, sensitivity analyses were conducted to assess the robustness of the MR analysis results. RESULTS IVW analysis results indicate a positive causal relationship between CTS and FS (p < 0.05, OR > 1), while a negative causal relationship between the two conditions was not observed. Heterogeneity tests suggest minimal heterogeneity in our IVW analysis results (p > 0.05). Multivariable MR testing also indicates no pleiotropy in our IVW analysis (p > 0.05), and stepwise exclusion tests demonstrate the reliability and stability of the MR analysis results. Gene Ontology (GO) pathway analysis reveals enrichment of genes regulated by the associated SNPs in the TGFβ-related pathways. CONCLUSION This study provides evidence of the genetic causal association between frozen shoulder and carpal tunnel syndrome and provides new insights into the genetics of fibrotic disorders.
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Affiliation(s)
- Yang Chen
- Department of Ultrasound, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaojin Wu
- Department of Ultrasound, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yongxing Zhang
- Department of Orthopedics, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jian Chen
- Department of Ultrasound, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Department of Ultrasound, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
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12
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Breeze CE, Haugen E, Gutierrez-Arcelus M, Yao X, Teschendorff A, Beck S, Dunham I, Stamatoyannopoulos J, Franceschini N, Machiela MJ, Berndt SI. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome Biol 2024; 25:3. [PMID: 38167104 PMCID: PMC10763681 DOI: 10.1186/s13059-023-03126-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.cancer.gov/ ; https://forge2.altiusinstitute.org/files/forgedb.html ; and https://doi.org/10.5281/zenodo.10067458 ), a standalone and web-based tool that integrates multiple datasets, delivering information on associated regulatory elements, transcription factor binding sites, and target genes for over 37 million variants. FORGEdb scores provide researchers with a quantitative assessment of the relative importance of each variant for targeted functional experiments.
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Affiliation(s)
- Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue 98121, Seattle, USA.
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue 98121, Seattle, USA
| | - María Gutierrez-Arcelus
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaozheng Yao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew Teschendorff
- CAS Key Lab of Computational Biology, Shanghai Institute for Biological Sciences, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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13
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Lv Y, Wen L, Hu WJ, Deng C, Ren HW, Bao YN, Su BW, Gao P, Man ZY, Luo YY, Li CJ, Xiang ZX, Wang B, Luan ZL. Schizophrenia in the genetic era: a review from development history, clinical features and genomic research approaches to insights of susceptibility genes. Metab Brain Dis 2024; 39:147-171. [PMID: 37542622 DOI: 10.1007/s11011-023-01271-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Schizophrenia is a devastating neuropsychiatric disorder affecting 1% of the world population and ranks as one of the disorders providing the most severe burden for society. Schizophrenia etiology remains obscure involving multi-risk factors, such as genetic, environmental, nutritional, and developmental factors. Complex interactions of genetic and environmental factors have been implicated in the etiology of schizophrenia. This review provides an overview of the historical origins, pathophysiological mechanisms, diagnosis, clinical symptoms and corresponding treatment of schizophrenia. In addition, as schizophrenia is a polygenic, genetic disorder caused by the combined action of multiple micro-effective genes, we further detail several approaches, such as candidate gene association study (CGAS) and genome-wide association study (GWAS), which are commonly used in schizophrenia genomics studies. A number of GWASs about schizophrenia have been performed with the hope to identify novel, consistent and influential risk genetic factors. Finally, some schizophrenia susceptibility genes have been identified and reported in recent years and their biological functions are also listed. This review may serve as a summary of past research on schizophrenia genomics and susceptibility genes (NRG1, DISC1, RELN, BDNF, MSI2), which may point the way to future schizophrenia genetics research. In addition, depending on the above discovery of susceptibility genes and their exact function, the development and application of antipsychotic drugs will be promoted in the future.
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Affiliation(s)
- Ye Lv
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Lin Wen
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Wen-Juan Hu
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Chong Deng
- Department of Neurosurgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Hui-Wen Ren
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ya-Nan Bao
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Bo-Wei Su
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ping Gao
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Zi-Yue Man
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yi-Yang Luo
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Cheng-Jie Li
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Zhi-Xin Xiang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Bing Wang
- Department of Endocrinology and Metabolism, The Central hospital of Dalian University of Technology, Dalian, 116000, China.
| | - Zhi-Lin Luan
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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14
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Rong JC, Chen XD, Jin NK, Hong J. Exploring the causal association of rheumatoid arthritis with atrial fibrillation: a Mendelian randomization study. Clin Rheumatol 2024; 43:29-40. [PMID: 37930596 DOI: 10.1007/s10067-023-06804-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND It has been proved that rheumatoid arthritis (RA) patients have high incidence of atrial fibrillation (AF). Nevertheless, whether they have causal relevance is uncertain. This study aimed to explore and verify the authenticity of causal relationship between RA and AF using Mendelian randomization (MR). METHODS The genome-wide association study (GWAS) summary data from Biobank Japan Project (BBJ) (RA, 4199 cases and 208,254 controls) were regarded as exposure data and the GWAS data from European Bio-informatics Institute database (EBI) (AF, 15,979 cases and 102,776 controls) as outcome data. The causal effect was appraised by the inverse variance weighted (IVW) method, MR-Egger regression, and weighted median estimator. MR-robust adjusted profile score (MR-RAPS) method was delivered to examine the robustness of causal relationship and MR Pleiotropy Residual Sum and Outlier (MR-PRESSO) method to control horizontal (directional) pleiotropy. RESULTS The results indicated that RA increased the risk of AF (IVW, the odds ratio (OR) = 1.060; 95% confidence interval (CI), 1.028 to 1.092; p = 1.411 × 10-4; weighted median, OR = 1.046, 95% CI, 1.002 to 1.093, p = 0.047). The MR analysis also showed this causal effect through all four IVW methods with various statistical algorithms. Both MR-RAPS and MR-PRESSO supported the causality of RA and AF. Also, the MR-PRESSO result indicated the absence of apparent pleiotropy. CONCLUSION There is a causal association between RA and AF. RA patients are genetically more vulnerable to AF. This study may contribute to further exploring early clinical prevention and fundamental mechanism of AF in patients with RA. Key Points • We provided some genetic evidence for the causal link between rheumatoid arthritis (RA) and atrial fibrillation (AF) with multiple Mendelian randomization (MR) methods. • RA patients were genetically more vulnerable to AF. • This study partly shed light on latent fundamental mechanisms underlying RA-induced AF and inspired future studies on RA-AF relationship.
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Affiliation(s)
- Jia-Cheng Rong
- Cardiovascular Department, Ningbo Hangzhou Bay Hospital, Hangzhou Bay New Area, Ningbo, Zhejiang, China
| | - Xu-Dong Chen
- Cardiovascular Department, Ningbo Hangzhou Bay Hospital, Hangzhou Bay New Area, Ningbo, Zhejiang, China
| | - Na-Ke Jin
- Cardiovascular Department, Ningbo Hangzhou Bay Hospital, Hangzhou Bay New Area, Ningbo, Zhejiang, China
| | - Jun Hong
- Cardiovascular Department, Ningbo Hangzhou Bay Hospital, Hangzhou Bay New Area, Ningbo, Zhejiang, China.
- Cardiovascular Department, Ningbo Hospital of Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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15
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Ohlei O, Sommerer Y, Dobricic V, Homann J, Deecke L, Schilling M, Bartrés-Faz D, Cattaneo G, Düzel S, Fjell AM, Lindenberger U, Pascual-Leone Á, Sedghpour Sabet S, Solé-Padullés C, Tormos JM, Vetter VM, Walhovd KB, Wesse T, Wittig M, Franke A, Demuth I, Lill CM, Bertram L. Genome-wide QTL mapping across three tissues highlights several Alzheimer's and Parkinson's disease loci potentially acting via DNA methylation. medRxiv 2023:2023.12.22.23300365. [PMID: 38196633 PMCID: PMC10775408 DOI: 10.1101/2023.12.22.23300365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
DNA methylation (DNAm) is an epigenetic mark with essential roles in disease development and predisposition. Here, we created genome-wide maps of methylation quantitative trait loci (meQTL) in three peripheral tissues and used Mendelian randomization (MR) analyses to assess the potential causal relationships between DNAm and risk for two common neurodegenerative disorders, i.e. Alzheimer's disease (AD) and Parkinson's disease (PD). Genome-wide single nucleotide polymorphism (SNP; ~5.5M sites) and DNAm (~850K CpG sites) data were generated from whole blood (n=1,058), buccal (n=1,527) and saliva (n=837) specimens. We identified between 11 and 15 million genome-wide significant (p<10-14) SNP-CpG associations in each tissue. Combining these meQTL GWAS results with recent AD/PD GWAS summary statistics by MR strongly suggests that the previously described associations between PSMC3, PICALM, and TSPAN14 and AD may be founded on differential DNAm in or near these genes. In addition, there is strong, albeit less unequivocal, support for causal links between DNAm at PRDM7 in AD as well as at KANSL1/MAPT in AD and PD. Our study adds valuable insights on AD/PD pathogenesis by combining two high-resolution "omics" domains, and the meQTL data shared along with this publication will allow like-minded analyses in other diseases.
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Affiliation(s)
- Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Yasmine Sommerer
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Jan Homann
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Laura Deecke
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Marcel Schilling
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - David Bartrés-Faz
- Department of Medicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain
| | - Gabriele Cattaneo
- Institut Guttmann, Institut Universitari de Neurorehabilitació adscrit a la UAB, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Camí de les Escoles, Badalona, Barcelona, Spain
| | - Sandra Düzel
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Anders M Fjell
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Álvaro Pascual-Leone
- Hinda and Arthur Marcus Institute for Aging Research and Deanna and Sidney Wolk Center for Memory Health, Hebrew SeniorLife, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Cristina Solé-Padullés
- Department of Medicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain
| | - Josep M Tormos
- Institut Guttmann, Institut Universitari de Neurorehabilitació adscrit a la UAB, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Camí de les Escoles, Badalona, Barcelona, Spain
| | - Valentin M Vetter
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases, Division of Lipid Metabolism, Charité-Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany
| | - Kristine B Walhovd
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Tanja Wesse
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Ilja Demuth
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases, Division of Lipid Metabolism, Charité-Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christina M Lill
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
- Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
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16
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Cao Z, Ma L, Cai W, Niu X, Yang N, Ni J, Wang X, Wei M, Chen S, Li Y. Genome-wide association study reveals HSF2, GJA1 and TRIM36 as susceptibility genes for preeclampsia: a community-based population study in Tianjin, China. Hypertens Pregnancy 2023; 42:2256863. [PMID: 37735976 DOI: 10.1080/10641955.2023.2256863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/04/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Preeclampsia (PE) mainly occurs in pregnant women and is hereditary. Several genome-wide association studies (GWAS) on Caucasian samples have reported some gene loci that are associated with preeclampsia. However, these studies have not reached consistent conclusions. No previous GWAS has examined preeclampsia in the Chinese Han population. METHOD This study aimed to identify common genetic variations associated with preeclampsia in the Chinese Han population through two-stage case‒control studies. The discovery cohort included 92 patients with severe preeclampsia and 187 healthy controls. The validation cohort included 52 patients with preeclampsia and 104 controls. A genome-wide association study was performed to identify putative preeclampsia genes in the discovery cohort, with validation in the validation cohort. RESULTS In the discovery cohort, GWAS demonstrated that 19 single-nucleotide polymorphisms (SNPs) were associated with preeclampsia (P < 10-5). The pathway analysis revealed that these 19 SNP representative genes were mainly enriched in the adenylyl cyclase-inhibiting G-protein coupled receptor signaling pathway. After validation in the validation cohort, rs13176432 and rs13210237 remained closely related to preeclampsia (P<0.05). In the combined data set, the frequency of the G allele in rs13176432 was significantly higher in cases with preeclampsia than in controls (P = 5 × 10-6). The frequency of the A allele in rs13210237 was higher in the preeclampsia group (P = 8 × 10-6). The rs13210237 representative genes include HSF2 and GJA1, while the rs13176432 representative gene is TRIM36. There were no differences in genotype distribution between the early-onset and late-onset preeclampsia groups (P > 0.05). Furthermore, rs13210237 and rs13176432 were related to preeclampsia in the adjusted regression model (P < 0.000). CONCLUSION In this study of two independent cohorts, we found that rs13210237 and rs13176432 might be novel preeclampsia-susceptible genetic factors in the Han population in China. However, there was no association between the onset of preeclampsia and these genotypes.
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Affiliation(s)
- Zhenhua Cao
- Nankai Hospital, Tianjin Medical University, Tianjin, China
- Department of cardiology, Nankai Hospital, Tianjin, China
| | - Li Ma
- Department of Obstetrics, The First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Cai
- Institute of Cardiovascular Disease and Heart Center, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, China
| | - Xiulong Niu
- Institute of Cardiovascular Disease and Heart Center, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, China
| | - Ning Yang
- Department of Cardiology, Tianjin Economic-Technological Development Area (TEDA) International Cardiovascular Hospital, Tianjin, China
| | - Jianmei Ni
- Department of cardiology, Nankai Hospital, Tianjin, China
| | - Xiaojing Wang
- Institute of Cardiovascular Disease and Heart Center, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, China
| | - Maoti Wei
- Department of Cardiology, Tianjin Economic-Technological Development Area (TEDA) International Cardiovascular Hospital, Tianjin, China
| | - Shaobo Chen
- Institute of Cardiovascular Disease and Heart Center, Characteristic Medical Center of the Chinese People's Armed Police Force, Tianjin, China
| | - Yuming Li
- Department of Cardiology, Tianjin Economic-Technological Development Area (TEDA) International Cardiovascular Hospital, Tianjin, China
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17
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Ben-Zvi I, Karasik D, Ackert-Bicknell CL. Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies. Curr Osteoporos Rep 2023; 21:650-659. [PMID: 37971665 DOI: 10.1007/s11914-023-00831-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW GWAS, as a largely correlational analysis, requires in vitro or in vivo validation. Zebrafish (Danio rerio) have many advantages for studying the genetics of human diseases. Since gene editing in zebrafish has been highly valuable for studying embryonic skeletal developmental processes that are prenatally or perinatally lethal in mammalian models, we are reviewing pros and cons of this model. RECENT FINDINGS The true power for the use of zebrafish is the ease by which the genome can be edited, especially using the CRISPR/Cas9 system. Gene editing, followed by phenotyping, for complex traits such as BMD, is beneficial, but the major physiological differences between the fish and mammals must be considered. Like mammals, zebrafish do have main bone cells; thus, both in vivo stem cell analyses and in vivo imaging are doable. Yet, the "long" bones of fish are peculiar, and their bone cavities do not contain bone marrow. Partial duplication of the zebrafish genome should be taken into account. Overall, small fish toolkit can provide unmatched opportunities for genetic modifications and morphological investigation as a follow-up to human-first discovery.
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Affiliation(s)
- Inbar Ben-Zvi
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - David Karasik
- The Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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18
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Guo F, Kang J, Xu J, Wei S, Tao J, Dong Y, Ma Y, Tian H, Guo X, Bi S, Zhang C, Lv H, Shang Z, Jiang Y, Zhang M. Genome-wide identification of m 6A-associated single nucleotide polymorphisms in complex diseases of nervous system. Neurosci Lett 2023; 817:137513. [PMID: 37827449 DOI: 10.1016/j.neulet.2023.137513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/11/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
N6-methyladenosine (m6A) is one of the most abundant chemical modifications on RNA and can affect the occurrence and development of diseases. Some studies have shown that the expressions of some m6A-related genes are significantly regulated by single nucleotide variants (SNV). However, the function of m6A-associated single nucleotide polymorphisms (m6A-SNP) remains unclear in multiple sclerosis (MS), Alzheimer's disease (AD) and Parkinson's disease (PD). Here, we identified the disease-associated m6A-SNPs by integrating genome-wide association study (GWAS) and m6A-SNPs from the RMVar database, and confirmed the relationship between these identified m6A-SNPs and their target genes in eQTL analysis and gene differential expression analysis. Finally, 26 genes corresponding to 20 m6A-SNPs with eQTL signals were identified and differentially expressed (P < 0.05) in MS, 15 genes corresponding to 12 m6A-SNPs (P < 1e-04) were differentially expressed in AD, and 27 PD-associated m6A-SNPs that regulated the expression of 31 genes were identified. There were 5 HLA genes with eQTL signals (HLA-DQB1, HLA-DRB1, HLA-DQA1, HLA-DQA2 and HLA-DQB1-AS1) to be detected in the three diseases. In summary, our study provided new insights into understanding the potential roles of these m6A-SNPs in disease pathogenesis as well as therapeutic target.
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Affiliation(s)
- Fei Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China
| | - Jingxuan Kang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China
| | - Jing Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junxian Tao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China
| | - Yu Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China
| | - Yingnan Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China
| | - Hongsheng Tian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xuying Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuo Bi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chen Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China.
| | - Mingming Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China; The EWAS Project, China.
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19
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Numaguchi K, Kitamura Y, Kashiwamoto T, Morimoto T, Oe T. Genomic region and origin for selected traits during differentiation of small-fruit cultivars in Japanese apricot (Prunus mume). Mol Genet Genomics 2023; 298:1365-1375. [PMID: 37632570 DOI: 10.1007/s00438-023-02062-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023]
Abstract
The Japanese apricot (Prunus mume) is a popular fruit tree in Japan. However, the genetic factors associated with fruit trait variations are poorly understood. In this study, we investigated nine fruit-associated traits, including harvesting time, fruit diameter, fruit shape, fruit weight, stone (endocarp) weight, ratio of stone weight to fruit weight, and rate of fruit gumming, using 110 Japanese apricot accessions over four years. A genome-wide association study (GWAS) was performed for these traits and strong signals were detected on chromosome 6 for harvesting time and fruit diameters. These peaks were shown to undergo strong artificial selection during the differentiation of small-fruit cultivars. The genomic region defined by the GWAS and XP-nSL analyses harbored several candidate genes associated with plant hormone regulation. Furthermore, the alleles of small-fruit cultivars in this region were shown to have genetic proximity to some Chinese cultivars of P. mume. These results indicate that the small-fruit trait originated in China; after being introduced into Japan, it was preferred and selected by the Japanese people, resulting in the differentiation of small-fruit cultivars.
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Affiliation(s)
- Koji Numaguchi
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan.
- Wakayama Fruit Tree Experiment Station, 751-1, Oki, Aridagawa-cho, Arida-gun, Wakayama, 643-0022, Japan.
| | - Yuto Kitamura
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Tomoaki Kashiwamoto
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
| | - Takuya Morimoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Kitainayazuma, Seika-cho, Soraku-gun, Kyoto, 619-0244, Japan
| | - Takaaki Oe
- Japanese Apricot Laboratory, Wakayama Fruit Tree Experiment Station, 1416-7 Higashi-Honjo, Minabe-cho, Hidaka-gun, Wakayama, 645-0021, Japan
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20
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Lee JB, Lim JH, Park HB. Genome-wide association studies to identify quantitative trait loci and positional candidate genes affecting meat quality-related traits in pigs. J Anim Sci Technol 2023; 65:1194-1204. [PMID: 38616878 PMCID: PMC11007289 DOI: 10.5187/jast.2023.e70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 04/16/2024]
Abstract
Meat quality comprises a set of key traits such as pH, meat color, water-holding capacity, tenderness and marbling. These traits are complex because they are affected by multiple genetic and environmental factors. The aim of this study was to investigate the molecular genetic basis underlying nine meat quality-related traits in a Yorkshire pig population using a genome-wide association study (GWAS) and subsequent biological pathway analysis. In total, 45,926 single nucleotide polymorphism (SNP) markers from 543 pigs were selected for the GWAS after quality control. Data were analyzed using a genome-wide efficient mixed model association (GEMMA) method. This linear mixed model-based approach identified two quantitative trait loci (QTLs) for meat color (b*) on chromosome 2 (SSC2) and one QTL for shear force on chromosome 8 (SSC8). These QTLs acted additively on the two phenotypes and explained 3.92%-4.57% of the phenotypic variance of the traits of interest. The genes encoding HAUS8 on SSC2 and an lncRNA on SSC8 were identified as positional candidate genes for these QTLs. The results of the biological pathway analysis revealed that positional candidate genes for meat color (b*) were enriched in pathways related to muscle development, muscle growth, intramuscular adipocyte differentiation, and lipid accumulation in muscle, whereas positional candidate genes for shear force were overrepresented in pathways related to cell growth, cell differentiation, and fatty acids synthesis. Further verification of these identified SNPs and genes in other independent populations could provide valuable information for understanding the variations in pork quality-related traits.
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Affiliation(s)
- Jae-Bong Lee
- Korea Zoonosis Research Institute (KoZRI),
Jeonbuk National University, Iksan 54531, Korea
| | - Ji-Hoon Lim
- Department of Animal Resources Science,
Kongju National University, Yesan 32439, Korea
| | - Hee-Bok Park
- Department of Animal Resources Science,
Kongju National University, Yesan 32439, Korea
- Resource Science Research Institute,
Kongju National University, Yesan 32439, Korea
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21
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Xu W, Huang H, Li X, Yang M, Chi S, Pan Y, Li N, Paterson AH, Chai Y, Lu K. CaHMA1 promotes Cd accumulation in pepper fruit. J Hazard Mater 2023; 460:132480. [PMID: 37683343 DOI: 10.1016/j.jhazmat.2023.132480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 09/10/2023]
Abstract
The main planting areas for pepper (Capsicum sp.) are high in cadmium (Cd), which is the most prevalent heavy metal pollutant worldwide. Breeding pepper cultivars with low Cd levels can promote sustainable agricultural production and ensure the safety of pepper products. To identify breeding targets for reducing Cd accumulation in pepper fruits, we performed a genome-wide association study on 186 accessions. Polymorphisms were associated with fruit Cd content in a genomic region containing a homolog of Arabidopsis (Arabidopsis thaliana) Heavy metal-transporting ATPase 1 (HMA1) encoding a P-type ATPase. In two cultivars with contrasting Cd accumulation, transcriptome analysis revealed differentially expressed genes enriched for carbohydrate metabolism and photosynthesis in fruits with high Cd accumulation, and a Cd2+/Zn2+-exporting ATPase gene (HMA). Heterologous expression of CaHMA1 in yeast increases Cd sensitivity. Overexpression of CaHMA1 conferred a severe increase in Cd content in Arabidopsis plants, whereas reduced CaHMA1 expression in pepper fruits decreased Cd content. We propose that CaHMA1 expression may be an important component of the high Cd accumulation in pepper plants.
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Affiliation(s)
- Weihong Xu
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - He Huang
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Mei Yang
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Sunlin Chi
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Yu Pan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Nannan Li
- College of Resources and Environmental Sciences, Southwest University, Chongqing 400715, China
| | - Andrew H Paterson
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA.
| | - Yourong Chai
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
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22
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Neumann A, Ohlei O, Küçükali F, Bos IJ, Timsina J, Vos S, Prokopenko D, Tijms BM, Andreasson U, Blennow K, Vandenberghe R, Scheltens P, Teunissen CE, Engelborghs S, Frisoni GB, Blin O, Richardson JC, Bordet R, Lleó A, Alcolea D, Popp J, Marsh TW, Gorijala P, Clark C, Peyratout G, Martinez-Lage P, Tainta M, Dobson RJB, Legido-Quigley C, Van Broeckhoven C, Tanzi RE, Ten Kate M, Lill CM, Barkhof F, Cruchaga C, Lovestone S, Streffer J, Zetterberg H, Visser PJ, Sleegers K, Bertram L. Multivariate GWAS of Alzheimer's disease CSF biomarker profiles implies GRIN2D in synaptic functioning. Genome Med 2023; 15:79. [PMID: 37794492 PMCID: PMC10548686 DOI: 10.1186/s13073-023-01233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) of Alzheimer's disease (AD) have identified several risk loci, but many remain unknown. Cerebrospinal fluid (CSF) biomarkers may aid in gene discovery and we previously demonstrated that six CSF biomarkers (β-amyloid, total/phosphorylated tau, NfL, YKL-40, and neurogranin) cluster into five principal components (PC), each representing statistically independent biological processes. Here, we aimed to (1) identify common genetic variants associated with these CSF profiles, (2) assess the role of associated variants in AD pathophysiology, and (3) explore potential sex differences. METHODS We performed GWAS for each of the five biomarker PCs in two multi-center studies (EMIF-AD and ADNI). In total, 973 participants (n = 205 controls, n = 546 mild cognitive impairment, n = 222 AD) were analyzed for 7,433,949 common SNPs and 19,511 protein-coding genes. Structural equation models tested whether biomarker PCs mediate genetic risk effects on AD, and stratified and interaction models probed for sex-specific effects. RESULTS Five loci showed genome-wide significant association with CSF profiles, two were novel (rs145791381 [inflammation] and GRIN2D [synaptic functioning]) and three were previously described (APOE, TMEM106B, and CHI3L1). Follow-up analyses of the two novel signals in independent datasets only supported the GRIN2D locus, which contains several functionally interesting candidate genes. Mediation tests indicated that variants in APOE are associated with AD status via processes related to amyloid and tau pathology, while markers in TMEM106B and CHI3L1 are associated with AD only via neuronal injury/inflammation. Additionally, seven loci showed sex-specific associations with AD biomarkers. CONCLUSIONS These results suggest that pathway and sex-specific analyses can improve our understanding of AD genetics and may contribute to precision medicine.
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Affiliation(s)
- Alexander Neumann
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, V50.2M, Lübeck, 23562, Germany
| | - Fahri Küçükali
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Isabelle J Bos
- Netherlands Institute for Health Services Research, Utrecht, Netherlands
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Stephanie Vos
- Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, Netherlands
| | - Ulf Andreasson
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Neurology Service, University Hospital Leuven, Leuven, Belgium
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, Netherlands
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, Netherlands
| | - Sebastiaan Engelborghs
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Universitair Ziekenhuis Brussel (UZ Brussel) and Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Giovanni B Frisoni
- Memory Center, Department of Rehabilitation and Geriatrics, Geneva University and University Hospitals, Geneva, Switzerland
| | - Oliver Blin
- Clinical Pharmacology & Pharmacovigilance Department, Marseille University Hospital, Marseille, France
| | | | - Régis Bordet
- Neuroscience & Cognition, CHU de Lille, University of Lille, Inserm, France
| | - Alberto Lleó
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Daniel Alcolea
- Memory Unit, Neurology Department, Hospital de Sant Pau, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Julius Popp
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zürich, Zurich, Switzerland
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Thomas W Marsh
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biology & Biomedical Sciences, Washington University in St. Louis, St Louis, MO, USA
| | - Priyanka Gorijala
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Christopher Clark
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zürich, Zurich, Switzerland
| | - Gwendoline Peyratout
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pablo Martinez-Lage
- Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, San Sebastian, Spain
| | - Mikel Tainta
- Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, San Sebastian, Spain
- Zumarraga Hospital, Osakidetza, Integrated Health Organization (OSI) Goierri-Urola Garia, Basque Country, Spain
| | - Richard J B Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Boston, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- Health Data Research UK London, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- The National Institute for Health Research University College London Hospitals Biomedical Research Centre, University College London, London, UK
| | - Cristina Legido-Quigley
- Steno Diabetes Center, Copenhagen, Denmark
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Christine Van Broeckhoven
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Rudolph E Tanzi
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Mara Ten Kate
- Alzheimer Center and Department of Neurology, VU University Medical Center, Amsterdam, Netherlands
- Department of Radiology and Nuclear Medicine, VU University Medical Center, Amsterdam, Netherlands
| | - Christina M Lill
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, V50.2M, Lübeck, 23562, Germany
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College, London, UK
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
- Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Simon Lovestone
- Janssen Medical Ltd, Wycombe, UK
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Johannes Streffer
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- AC Immune SA, Lausanne, Switzerland
- Janssen R&D, LLC, Beerse, Belgium
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- UK Dementia Research Institute, University College London, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Pieter Jelle Visser
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Alzheimer Centrum Limburg, Maastricht University, Maastricht, Netherlands
- Alzheimer Center and Department of Neurology, VU University Medical Center, Amsterdam, Netherlands
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, V50.2M, Lübeck, 23562, Germany.
- Centre for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway.
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Zhang F, Deng S, Zhang J, Xu W, Xian D, Wang Y, Zhao Q, Liu Y, Zhu X, Peng M, Zhang L. Causality between heart failure and epigenetic age: a bidirectional Mendelian randomization study. ESC Heart Fail 2023; 10:2903-2913. [PMID: 37452462 PMCID: PMC10567637 DOI: 10.1002/ehf2.14446] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/01/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
AIMS Heart failure (HF) is a prevalent age-related cardiovascular disease with poor prognosis in the elderly population. This study aimed to establish the causal relationship between ageing and HF by conducting a bidirectional Mendelian randomization (MR) analysis on epigenetic age (a marker of ageing) and HF. METHODS AND RESULTS Genome-wide association study data for epigenetic age (GrimAge, HorvathAge, HannumAge, and PhenoAge) and HF were collected and assessed for significant genetic variables. A bidirectional MR analysis was carried out using the random-effects inverse-variance weighted (IVW) method as the primary approach, while other methods (MR-Egger, weighted median, simple mode, and weighted mode) and multiple sensitivity analyses (heterogeneity analysis, leave-one-out sensitivity analysis, and horizontal pleiotropy analysis) were employed to evaluate the impact of epigenetic age on HF and vice versa. Bidirectional MR analysis of two samples revealed that the epigenetic PhenoAge clock increased the risk of HF [IVW odds ratio (OR) 1.015, 95% confidence interval (CI) 1.002-1.028, P = 0.028 and weighted median OR 1.020, 95% CI 1.001-1.038, P = 0.039]. Other results were not statistically significant. CONCLUSIONS The bidirectional MR analysis demonstrated a causal link between genetically predicted epigenetic age and HF in individuals of European descent. Further research into epigenetic age in other populations and additional genetic information related to HF is warranted.
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Affiliation(s)
- Fengjun Zhang
- College of Acupuncture and MassageShandong University of Traditional Chinese MedicineJinanChina
| | - Shanshan Deng
- Non‐Coding RNA and Drug Discovery Key Laboratory of Sichuan ProvinceChengdu Medical CollegeChengduChina
- School of Basic Medical SciencesChengdu Medical CollegeChengduChina
| | - Jing Zhang
- Department of PediatricsShandong Second Provincial General HospitalJinanChina
| | - Wenchang Xu
- College of Acupuncture and MassageShandong University of Traditional Chinese MedicineJinanChina
| | - Dexian Xian
- College of Acupuncture and MassageShandong University of Traditional Chinese MedicineJinanChina
| | - Yuxuan Wang
- College of Traditional Chinese MedicineShandong University of Traditional Chinese MedicineJinanChina
| | - Qiong Zhao
- Department of Traditional Chinese MedicineShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Yuan Liu
- Department of Traditional Chinese MedicineShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Xiuli Zhu
- Department of Radiation Oncology and Shandong Province Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and InstituteShandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Min Peng
- Department of Traditional Chinese MedicineShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
| | - Lin Zhang
- Department of Clinical Pharmacy, Shaoxing People's Hospital, Shaoxing HospitalZhejiang University School of MedicineShaoxingChina
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24
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Zheng Y, Thi KM, Lin L, Xie X, Khine EE, Nyein EE, Lin MHW, New WW, Aye SS, Wu W. Genome-wide association study of cooking-caused grain expansion in rice ( Oryza sativa L.). Front Plant Sci 2023; 14:1250854. [PMID: 37711286 PMCID: PMC10498926 DOI: 10.3389/fpls.2023.1250854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.
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Affiliation(s)
- Yan Zheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Khin Mar Thi
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lihui Lin
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ei Ei Khine
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ei Ei Nyein
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Min Htay Wai Lin
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - Win Win New
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - San San Aye
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - Weiren Wu
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Yuan P, Liu H, Wang X, Hammond JP, Shi L. Genome-wide association study reveals candidate genes controlling root system architecture under low phosphorus supply at seedling stage in Brassica napus. Mol Breed 2023; 43:63. [PMID: 37521313 PMCID: PMC10382450 DOI: 10.1007/s11032-023-01411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Optimal root system architecture (RSA) is essential for vigorous growth and yield in crops. Plants have evolved adaptive mechanisms in response to low phosphorus (LP) stress, and one of those is changes in RSA. Here, more than five million single-nucleotide polymorphisms (SNPs) obtained from whole-genome re-sequencing data (WGR) of an association panel of 370 oilseed rape (Brassica napus L.) were used to conduct a genome-wide association study (GWAS) of RSA traits of the panel at LP in "pouch and wick" system. Fifty-two SNPs were forcefully associated with lateral root length (LRL), total root length (TRL), lateral root density (LRD), lateral root number (LRN), mean lateral root length (MLRL), and root dry weight (RDW) at LP. There were significant correlations between phenotypic variation and the number of favorable alleles of the associated loci on chromosomes A06 (chrA06_20030601), C03 (chrC03_3535483), and C07 (chrC07_42348561), respectively. Three candidate genes (BnaA06g29270D, BnaC03g07130D, and BnaC07g43230D) were detected by combining transcriptome, candidate gene association analysis, and haplotype analysis. Cultivar carrying "CCGC" at BnaA06g29270DHap1, "CAAT" at BnaC03g07130DHap1, and "ATC" at BnaC07g43230DHap1 had greater LRL, LRN, and RDW than lines carrying other haplotypes at LP supply. The RSA of a cultivar harboring the three favorable haplotypes was further confirmed by solution culture experiments. These findings define exquisite insights into genetic architectures underlying B. napus RSA at LP and provide valuable gene resources for root breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01411-2.
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Affiliation(s)
- Pan Yuan
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
| | - Haijiang Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaohua Wang
- College of Agriculture and Forestry Science, Linyi University, Linyi, 276000 China
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR UK
| | - Lei Shi
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
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26
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Liu D, Tan W, Wang H, Li W, Fu J, Li J, Zhou Y, Lin M, Xing W. Genetic diversity and genome-wide association study of 13 agronomic traits in 977 Beta vulgaris L. germplasms. BMC Genomics 2023; 24:413. [PMID: 37488485 PMCID: PMC10364417 DOI: 10.1186/s12864-023-09522-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Sugar beet (Beta vulgaris L.) is an economically essential sugar crop worldwide. Its agronomic traits are highly diverse and phenotypically plastic, influencing taproot yield and quality. The National Beet Medium-term Gene Bank in China maintains more than 1700 beet germplasms with diverse countries of origin. However, it lacks detailed genetic background associated with morphological variability and diversity. RESULTS Here, a comprehensive genome-wide association study (GWAS) of 13 agronomic traits was conducted in a panel of 977 sugar beet accessions. Almost all phenotypic traits exhibited wide genetic diversity and high coefficient of variation (CV). A total of 170,750 high-quality single-nucleotide polymorphisms (SNPs) were obtained using the genotyping-by-sequencing (GBS). Neighbour-joining phylogenetic analysis, principal component analysis, population structure and kinship showed no obvious relationships among these genotypes based on subgroups or regional sources. GWAS was carried out using a mixed linear model, and 159 significant associations were detected for these traits. Within the 25 kb linkage disequilibrium decay of the associated markers, NRT1/PTR FAMILY 6.3 (BVRB_5g097760); nudix hydrolase 15 (BVRB_8g182070) and TRANSPORT INHIBITOR RESPONSE 1 (BVRB_8g181550); transcription factor MYB77 (BVRB_2g023500); and ethylene-responsive transcription factor ERF014 (BVRB_1g000090) were predicted to be strongly associated with the taproot traits of root groove depth (RGD); root shape (RS); crown size (CS); and flesh colour (FC), respectively. For the aboveground traits, UDP-glycosyltransferase 79B6 (BVRB_9g223780) and NAC domain-containing protein 7 (BVRB_5g097990); F-box protein At1g10780 (BVRB_6g140760); phosphate transporter PHO1 (BVRB_3g048660); F-box protein CPR1 (BVRB_8g181140); and transcription factor MYB77 (BVRB_2g023500) and alcohol acyltransferase 9 (BVRB_2g023460) might be associated with the hypocotyl colour (HC); plant type (PT); petiole length (PL); cotyledon size (C); and fascicled leaf type (FLT) of sugar beet, respectively. AP-2 complex subunit mu (BVRB_5g106130), trihelix transcription factor ASIL2 (BVRB_2g041790) and late embryogenesis abundant protein 18 (BVRB_5g106150) might be involved in pollen quantity (PQ) variation. The candidate genes extensively participated in hormone response, nitrogen and phosphorus transportation, secondary metabolism, fertilization and embryo maturation. CONCLUSIONS The genetic basis of agronomical traits is complicated in heterozygous diploid sugar beet. The putative valuable genes found in this study will help further elucidate the molecular mechanism of each phenotypic trait for beet breeding.
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Affiliation(s)
- Dali Liu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wenbo Tan
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Hao Wang
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Wangsheng Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jingjing Fu
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Jiajia Li
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China
| | - Yuanhang Zhou
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Ming Lin
- Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, P. R. China
| | - Wang Xing
- National Beet Medium-term Gene Bank, Heilongjiang University, Harbin, 150080, P. R. China.
- Key Laboratory of Sugar Beet Genetics and Breeding, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, 150080, P. R. China.
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Zhou XY, Liu RK, Zeng CP. Exploring the novel SNPs in neuroticism and birth weight based on GWAS datasets. BMC Med Genomics 2023; 16:167. [PMID: 37454083 PMCID: PMC10349512 DOI: 10.1186/s12920-023-01591-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Epidemiological studies have confirmed that low birth weight (BW) is related to neuroticism and they may have a common genetic mechanism based on phenotypic correlation research. We conducted our study on a European population with 159,208 neuroticism and 289,142 birth weight samples. In this study, we aimed to identify new neuroticism single nucleotide polymorphisms (SNPs) and pleiotropic SNPs associated with neuroticism and BW and to provide more theoretical basis for the pathogenesis of the disease. METHODS We estimated the pleiotropic enrichment between neuroticism and BW in two independent Genome-wide association studies (GWAS) when the statistical thresholds were Conditional False Discovery Rate (cFDR) < 0.01 and Conjunctional Conditional False Discovery Rate (ccFDR) < 0.05. We performed gene annotation and gene functional analysis on the selected significant SNPs to determine the biological role of gene function and pathogenesis. Two-sample Mendelian Randomization (TSMR) analysis was performed to explore the causal relationship between the neuroticism and BW. RESULTS The conditional quantile-quantile plots (Q-Q plot) indicated that neuroticism and BW have strong genetic pleiotropy enrichment trends. With the threshold of cFDR < 0.001, we identified 126 SNPs related to neuroticism and 172 SNPs related to BW. With the threshold of ccFDR < 0.05, we identified 62 SNPs related to both neuroticism and BW. Among these SNPs, rs8039305 and rs35755513 have eQTL (expressed quantitative trait loci) and meQTL (methylation quantitative trait loci) effects simultaneously. Through GO enrichment analysis we also found that the two pathways of positive regulation of "mesenchymal cell proliferation" and "DNA-binding transcription factor activity" were significantly enriched in neuroticism and BW. Mendelian randomization analysis results indicate that there is no obvious causal relationship between neuroticism and birth weight. CONCLUSION We found 126 SNPs related to neuroticism, 172 SNPs related to BW and 62 SNPs associated with both neuroticism and BW, which provided a theoretical basis for their genetic mechanism and novel potential targets for treatment/intervention development.
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Affiliation(s)
- Xiao-Ying Zhou
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510330, China
- Department of Endocrinology and Metabolism, SSL Central Hospital of Dongguan City, No.1, Xianglong Road, Dongguan, 523326, China
| | - Rui-Ke Liu
- Department of Endocrinology and Metabolism, SSL Central Hospital of Dongguan City, No.1, Xianglong Road, Dongguan, 523326, China.
| | - Chun-Ping Zeng
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510330, China.
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Zhang H, Yao Y, Zhong X, Meng F, Hemminki K, Qiu J, Shu X. Association between intake of the n-3 polyunsaturated fatty acid docosahexaenoic acid (n-3 PUFA DHA) and reduced risk of ovarian cancer: A systematic Mendelian Randomization study. Clin Nutr 2023; 42:1379-1388. [PMID: 37421851 DOI: 10.1016/j.clnu.2023.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND & AIMS Whether the intake of docosahexaenoic acid (DHA), an n-3 polyunsaturated fatty acid, is beneficial for ovarian cancer (OC) remains controversial and we hope to disentangle this puzzle using genetic data from large-scale populations in European and Asian. METHODS We employed, for the first time, a systematic Mendelian randomization (MR) design to comprehensively evaluate the causal effect of plasma DHA levels, an objective biomarker of DHA intake, on OC risk in European and then verified the extrapolation of the results in the Asian. Data in the analysis included genetic association data obtained from large-scale genome-wide association studies with 13,499 individuals for plasma DHA measurements and 66,450 individuals for OC in the European population, and 1361 individuals for plasma DHA measurements and 61,457 individuals for OC in the Asian population. The causal relationship between DHA and OC was estimated using the inverse-variance weighted approach, together with extensive validation and sensitivity analyses to verify the main results. RESULTS In the European population, MR evidence suggested a causal relationship between higher plasma DHA levels and lower OC risk (OR, 0.89 for OC per one-SD increment in DHA; 95% CI, 0.83 to 0.96; P = 0.003). Subgroup analysis by histological type of OC indicated that this observed association was stronger among endometrioid ovarian cancer (EOC) (OR, 0.82; 95% CI, 0.69 to 0.96; P = 0.014). A similar causal association of borderline significance was reached in the Asian replication set. The above results were consistently supported by a series of validation and sensitivity analyses. CONCLUSION Our study provided robust genetic evidence for a protective association between plasma DHA levels and lower risk of OC, especially EOC, in the European population. These findings may inform prevention strategies and interventions directed towards DHA intake and OC.
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Affiliation(s)
- Haifeng Zhang
- Department of Epidemiology, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Yinshuang Yao
- Department of Epidemiology, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Xiaoyan Zhong
- Department of Toxicology, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Fang Meng
- National Key Laboratory of Immunity and Inflammation, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, China; State Key Laboratory of Medical Molecular Biology, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, China
| | - Kari Hemminki
- Biomedical Center, Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605, Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
| | - Junlan Qiu
- Department of Oncology and Hematology, the Affiliated Suzhou Hospital of Nanjing University Medical School, Suzhou, 215153, China.
| | - Xiaochen Shu
- Department of Epidemiology, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, 215123, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, 215123, China.
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29
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Hess T, Maj C, Gehlen J, Borisov O, Haas SL, Gockel I, Vieth M, Piessen G, Alakus H, Vashist Y, Pereira C, Knapp M, Schüller V, Quaas A, Grabsch HI, Trautmann J, Malecka-Wojciesko E, Mokrowiecka A, Speller J, Mayr A, Schröder J, Hillmer AM, Heider D, Lordick F, Pérez-Aísa Á, Campo R, Espinel J, Geijo F, Thomson C, Bujanda L, Sopeña F, Lanas Á, Pellisé M, Pauligk C, Goetze TO, Zelck C, Reingruber J, Hassanin E, Elbe P, Alsabeah S, Lindblad M, Nilsson M, Kreuser N, Thieme R, Tavano F, Pastorino R, Arzani D, Persiani R, Jung JO, Nienhüser H, Ott K, Schumann RR, Kumpf O, Burock S, Arndt V, Jakubowska A, Ławniczak M, Moreno V, Martín V, Kogevinas M, Pollán M, Dąbrowska J, Salas A, Cussenot O, Boland-Auge A, Daian D, Deleuze JF, Salvi E, Teder-Laving M, Tomasello G, Ratti M, Senti C, De Re V, Steffan A, Hölscher AH, Messerle K, Bruns CJ, Sīviņš A, Bogdanova I, Skieceviciene J, Arstikyte J, Moehler M, Lang H, Grimminger PP, Kruschewski M, Vassos N, Schildberg C, Lingohr P, Ridwelski K, Lippert H, Fricker N, Krawitz P, Hoffmann P, Nöthen MM, Veits L, Izbicki JR, Mostowska A, Martinón-Torres F, Cusi D, Adolfsson R, Cancel-Tassin G, Höblinger A, Rodermann E, Ludwig M, Keller G, Metspalu A, Brenner H, Heller J, Neef M, Schepke M, Dumoulin FL, Hamann L, Cannizzaro R, Ghidini M, Plaßmann D, Geppert M, Malfertheiner P, Gehlen O, Skoczylas T, Majewski M, Lubiński J, Palmieri O, Boccia S, Latiano A, Aragones N, Schmidt T, Dinis-Ribeiro M, Medeiros R, Al-Batran SE, Leja M, Kupcinskas J, García-González MA, Venerito M, Schumacher J. Dissecting the genetic heterogeneity of gastric cancer. EBioMedicine 2023; 92:104616. [PMID: 37209533 DOI: 10.1016/j.ebiom.2023.104616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture. METHODS We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO. FINDINGS Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level. INTERPRETATION Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO. FUNDING German Research Foundation (DFG).
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Affiliation(s)
- Timo Hess
- Institute of Human Genetics, University of Marburg, Marburg, Germany; Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute of Human Genetics, University of Marburg, Marburg, Germany; Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Jan Gehlen
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Oleg Borisov
- Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Stephan L Haas
- Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Stockholm, Sweden
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Michael Vieth
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuernberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Guillaume Piessen
- Department of Digestive and Oncological Surgery, Claude Huriez Hospital, CHU Lille, Lille, France
| | - Hakan Alakus
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany; Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Carina Pereira
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Porto 4200-072, Portugal; Porto Comprehensive Cancer Center & RISE @ CI-IPO, University of Porto, Porto 4200-450, Portugal
| | - Michael Knapp
- Medical Faculty, Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), University of Bonn, Bonn, Germany
| | - Vitalia Schüller
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Alexander Quaas
- Medical Faculty, Institute of Pathology, University Hospital Cologne, University of Cologne, Germany
| | - Heike I Grabsch
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands; Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jessica Trautmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | | | - Anna Mokrowiecka
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Jan Speller
- Medical Faculty, Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), University of Bonn, Bonn, Germany
| | - Andreas Mayr
- Medical Faculty, Institute of Medical Biometrics, Informatics and Epidemiology (IMBIE), University of Bonn, Bonn, Germany
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Axel M Hillmer
- Medical Faculty, Institute of Pathology, University Hospital Cologne, University of Cologne, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Florian Lordick
- University Cancer Center Leipzig, Leipzig University Medical Center, Leipzig, Germany
| | | | - Rafael Campo
- Department of Gastroenterology, Hospital Parc Tauli, Sabadell, Spain
| | - Jesús Espinel
- Department of Gastroenterology, Complejo Hospitalario, León, Spain
| | - Fernando Geijo
- Department of Gastroenterology, Hospital Clínico Universitario, Salamanca, Spain
| | - Concha Thomson
- Department of Gastroenterology, Hospital Obispo Polanco, Teruel, Spain
| | - Luis Bujanda
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Federico Sopeña
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | - Ángel Lanas
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - María Pellisé
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Department of Gastroenterology, Hospital Clinic of Barcelona, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Claudia Pauligk
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Thorsten Oliver Goetze
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Carolin Zelck
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Julian Reingruber
- Institute of Human Genetics, University of Marburg, Marburg, Germany
| | - Emadeldin Hassanin
- Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter Elbe
- Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Stockholm, Sweden
| | - Sandra Alsabeah
- Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital and Unit of Gastroenterology and Rheumatology, Stockholm, Sweden
| | - Mats Lindblad
- Division of Surgery, Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nilsson
- Division of Surgery, Department of Upper GI Diseases, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Kreuser
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Francesca Tavano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Roberta Pastorino
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Dario Arzani
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Roberto Persiani
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Roma, Italy; Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Jin-On Jung
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany; Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Henrik Nienhüser
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Katja Ott
- Department of Surgery, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Ralf R Schumann
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oliver Kumpf
- Department of Anaesthesiology and Operative Intensive Care Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Poland
| | - Małgorzta Ławniczak
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, Poland
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Hospital Duran I Reynals, Barcelona, Spain; Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; Faculty of Medicine, Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
| | - Vicente Martín
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; The Research Group in Gene - Environment and Health Interactions (GIIGAS)/Institute of Biomedicine (IBIOMED), Universidad de Leon, Leon, Spain; Faculty of Health Sciences, Department of Biomedical Sciences, Area of Preventive Medicine and Public Health, Universidad de Leon, Leon, Spain
| | - Manolis Kogevinas
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Campus Del Mar, Barcelona, Spain; IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Spain
| | - Marina Pollán
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; Cancer and Environmental Epidemiology Unit, Department of Epidemiology of Chronic Diseases, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poland
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Olivier Cussenot
- CeRePP, Paris, France; GRC n°5 Predictive Onco-Urology, Tenon Hospital, Sorbonne University, Paris, France
| | - Anne Boland-Auge
- Centre National de Recherche en Génomique Humaine, CEA, University Paris-Saclay, Evry, France
| | - Delphine Daian
- Centre National de Recherche en Génomique Humaine, CEA, University Paris-Saclay, Evry, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine, CEA, University Paris-Saclay, Evry, France
| | - Erika Salvi
- Neuroalgology Unit Fondazione IRCCS, Instituto Neurologico 'Carlo Besta' Milan, Milan, Italy
| | - Maris Teder-Laving
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Gianluca Tomasello
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Medical Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Chiara Senti
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Department of Medical Oncology, Institut Jules Bordet - Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Valli De Re
- Unit of Immunopathologia e Biomarcatori Oncologici/Bio-proteomics Facility, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Agostino Steffan
- Unit of Immunopathologia e Biomarcatori Oncologici, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Arnulf H Hölscher
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | - Katharina Messerle
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany
| | | | - Armands Sīviņš
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia
| | - Inga Bogdanova
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia
| | - Jurgita Skieceviciene
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Justina Arstikyte
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Markus Moehler
- Department of Medicine I, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Peter P Grimminger
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Martin Kruschewski
- Department of General and Visceral Surgery, Klinikum Frankfurt (Oder), Germany
| | - Nikolaos Vassos
- Division of Surgical Oncology and Thoracic Surgery, Department of Surgery, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Claus Schildberg
- Department of General Surgery, Brandenburg Medical School Theodor Fontane, University Hospital Brandenburg, Brandenburg, Germany
| | - Philipp Lingohr
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, Bonn, Germany
| | - Karsten Ridwelski
- Department of General and Visceral Surgery, Klinikum Magdeburg GmbH, Magdeburg, Germany
| | - Hans Lippert
- Institute of Quality Assurance in Operative Medicine, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Nadine Fricker
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Peter Krawitz
- Medical Faculty, Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Lothar Veits
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuernberg, Klinikum Bayreuth, Bayreuth, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poland
| | - Federico Martinón-Torres
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Department of Pediatrics, Translational Pediatrics and Infectious Diseases Section, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Spain; Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Daniele Cusi
- Institute of Biomedical Technologies, National Research Council of Italy, Milan, Italy; Bio4Dreams-Business, Nursery for Life Sciences, Milan, Italy
| | - Rolf Adolfsson
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Geraldine Cancel-Tassin
- CeRePP, Paris, France; GRC n°5 Predictive Onco-Urology, Tenon Hospital, Sorbonne University, Paris, France
| | - Aksana Höblinger
- Department of Internal Medicine I, Community Hospital Mittelrhein, Koblenz, Germany
| | - Ernst Rodermann
- Association of Medical Practices in Hematology and Internal Oncology, Troisdorf, Germany
| | - Monika Ludwig
- Association for Oncological Studies (Gefos), Dortmund, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joerg Heller
- Department of Gastroenterology, Marienhaus Hospital Ahrweiler, Ahrweiler, Germany
| | - Markus Neef
- Department of Gastroenterology, Helios Hospital Siegburg, Siegburg, Germany
| | - Michael Schepke
- Department of Gastroenterology, Helios Hospital Siegburg, Siegburg, Germany
| | | | - Lutz Hamann
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato Cannizzaro
- Unit of Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Michele Ghidini
- Medical Oncology Unit, ASST of Cremona, Cremona, Italy; Medical Oncology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany; Department of Internal Medicine II, Hospital of the Ludwig Maximilians University of Munich, Munich, Germany
| | - Olivier Gehlen
- Department of Surgical Oncology, Centre Hospitalier Lyon-sud, Lyon, France
| | - Tomasz Skoczylas
- 2nd Department of General Surgery, Medical University of Lublin, Lublin, Poland
| | - Marek Majewski
- 2nd Department of General Surgery, Medical University of Lublin, Lublin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Poland
| | - Orazio Palmieri
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefania Boccia
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Anna Latiano
- Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Nuria Aragones
- Consortium for Biomedical Research in Epidemiology & Public Health (CIBER en Epidemiología y Salud Pública e CIBERESP), Spain; Epidemiology Section, Public Health Division, Department of Health of Madrid, Madrid, Spain
| | - Thomas Schmidt
- Department of General, Visceral, Cancer and Transplant Surgery, University of Cologne, Cologne, Germany; Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Mário Dinis-Ribeiro
- Porto Comprehensive Cancer Center & RISE @ CI-IPO, University of Porto, Porto 4200-450, Portugal; Gastroenterology Department, Portuguese Institute of Oncology of Porto, Porto 4200-072, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Porto 4200-072, Portugal; Research Department of the Portuguese League Against Cancer-North (LPCC-NRNorte), Porto 4200-177, Portugal
| | - Salah-Eddin Al-Batran
- Krankenhaus Nordwest, University Cancer Center, Frankfurt, Germany; Institut für Klinische Krebsforschung IKF GmbH am Krankenhaus Nordwest, Frankfurt, Germany
| | - Mārcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga East University Hospital, Riga, Latvia; Digestive Diseases Centre GASTRO, Riga, Latvia
| | - Juozas Kupcinskas
- Gastroenterology Department and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - María A García-González
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
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Kim YJ, Cho YS. Genetic association study identifies genetic variants for non-alcoholic fatty liver without comorbidities in the Korean population. Genes Genomics 2023:10.1007/s13258-023-01391-9. [PMID: 37133724 DOI: 10.1007/s13258-023-01391-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/15/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Non-alcoholic fatty liver (NAFL) refers to a disease in which fat builds up in the liver, similar to what occurs for those who drink a lot of alcohol, even in cases of not drinking alcohol at all or only in a small amount. Along with non-alcoholic steatohepatitis (NASH), NAFL is a type of non-alcoholic fatty liver disease (NAFLD). Currently, the prevalence of NAFLD is increasing worldwide. A wide range of comorbidities that can increase the risk of NAFLD includes obesity, type 2 diabetes, dyslipidemia, and metabolic syndrome. OBJECTIVE This study aimed to discover genetic variants for NAFL in the Korean population. METHODS Differing from previous studies, we conducted a genome-wide association study for NAFL in the selected subjects without comorbidities to rule out bias due to the inclusion of confounding effects of comorbidities. We grouped 424 NAFL cases and 5,402 controls from the Korean Genome and Epidemiology Study (KoGES) subjects without comorbidities such as dyslipidemia, type 2 diabetes, and metabolic syndrome. All subjects including cases and controls did not consume alcohol at all, or consumed less than 20 g/day for men and less than 10 g/day for women. RESULTS The logistic association analysis adjusting for sex, age, BMI, and waist circumference identified one novel genome-wide significant variant (rs7996045, P = 2.3 × 10-8) for NAFL. This variant was located in the intron of CLDN10 and was not detected using previous conventional approaches in which confounding effects resulting from comorbidities were not considered in the study design stage. In addition, we detected several genetic variants showing suggestive association for NAFL (P < 10-5). CONCLUSION The unique strategy in our association analysis of excluding major confounding factors provides, for the first time, an insight into the genuine genetic basis influencing NAFL.
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Affiliation(s)
- Yeon Jun Kim
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea.
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Chen Y, Niu S, Deng X, Song Q, He L, Bai D, He Y. Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing. BMC Plant Biol 2023; 23:196. [PMID: 37046207 PMCID: PMC10091845 DOI: 10.1186/s12870-023-04192-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou. RESULTS In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis. CONCLUSIONS In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.
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Affiliation(s)
- Yanjun Chen
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Xinyue Deng
- School of Architecture, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Limin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
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Xu P, Li H, Xu K, Cui X, Liu Z, Wang X. Genetic variation in BnGRP1 contributes to low phosphorus tolerance in Brassica napus. J Exp Bot 2023:erad114. [PMID: 36964902 DOI: 10.1093/jxb/erad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Indexed: 06/18/2023]
Abstract
Lack of phosphorus (P) is a major environmental factor affecting rapeseed (Brassica napus. L) root growth and development. For breeding purposes, it is crucial to identify the molecular mechanisms of root system architecture (RSA) traits underlying low P tolerance in rapeseed. The natural variations in the glycine-rich protein gene, BnGRP1, were analyzed in the natural population of 400 rapeseed cultivars under low P stress through genome-wide association study (GWAS) and transcriptome analyses. Based on 11 SNP mutations in BnGRP1 sequence, ten types of haplotypes (Hap) were formed. Compared with the other types, the cultivar of BnGRP1Hap1 type in the panel demonstrated the longest root length and heaviest root weight. BnGRP1Hap1 overexpression in rapeseed depicted the ability to enhance its resistance in response to low P tolerance. CRISPR/Cas9-derived BnGRP1Hap4 knockout mutations in rapeseed can lead to sensitivity to low P stress. Furthermore, BnGRP1Hap1 influences the expression of phosphate transporter 1 (PHT1) genes associated with P absorption. Overall, the findings of this study highlight new mechanisms of GRP1 genes in enhancing low P tolerance in rapeseed.
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Affiliation(s)
- Ping Xu
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Haiyuan Li
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Ke Xu
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Xiaoyu Cui
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Zhenning Liu
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Xiaohua Wang
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
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He J, Gai J. Genome-Wide Association Studies (GWAS). Methods Mol Biol 2023; 2638:123-46. [PMID: 36781639 DOI: 10.1007/978-1-0716-3024-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Most of the breeding targets are quantitative traits. In exploring the quantitative trait locus (QTL) system of a trait, linkage mapping was established using sparse polymerase chain reaction (PCR) markers. With the genome-wide sequencing technology advanced, genome-wide association study (GWAS) was developed for natural (germplasm) populations using dense genomic markers, which facilitates the identification of the complete QTL system with their multiple alleles on genomic locations. GWAS makes use of the linkage disequilibrium (LD) due to historical saturate recombination and high-density genomic markers to detect QTLs through statistical test for the association between molecular markers and phenotypes. However, due to inbreeding and mixture of source populations, the germplasm population often has complex and unknown structure, which leads to false positives/negatives in GWAS. Various GWAS methods have been proposed to reduce false positives/negatives, including those of the general linear model and the mixed linear model, which focused mainly on finding a handful of major QTLs under single-locus model for major gene cloning and could not detect directly the multiple alleles using bi-allelic single-nucleotide polymorphism (SNP) marker. As a relatively thorough detection of QTLs with their multiple alleles is required for germplasm population, the restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS) procedure was proposed for identifying the QTL system with varying multiple alleles. From the RTM-GWAS results, a QTL-allele matrix is constructed as a compact form of the population genetic constitution, which can be further used for crop genetic and breeding studies, including major gene mining, population evolution, and breeding by genetic design.
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Guo X, Ge Z, Wang M, Zhao M, Pei Y, Song X. Genome-wide association study of quality traits and starch pasting properties of maize kernels. BMC Genomics 2023; 24:59. [PMID: 36732681 PMCID: PMC9893588 DOI: 10.1186/s12864-022-09031-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/21/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Starch are the main nutritional components of maize (Zea mays L.), and starch pasting properties are widely used as essential indicators for quality estimation. Based on the previous studies, various genes related to pasting properties have been identified in maize. However, the loci underlying variations in starch pasting properties in maize inbred lines remain to be identified. RESULTS To investigate the genetic architecture of these traits, the starch pasting properties were examined based on 292 maize inbred lines, which were genotyped with the MaizeSNP50 BeadChip composed of 55,126 evenly spaced, random SNPs. A genome-wide association study (GWAS) implemented in the software package FarmCPU was employed to identify genomic loci for the starch pasting properties. 48 SNPs were found to be associated with pasting properties. Moreover, 37 candidate genes were correlated with pasting properties. Among the candidate genes, GRMZM2G143646 and GRMZM2G166407 were associated with breakdown and final viscosity significantly, and both genes encode PPR (Pentatricopeptide repeat) protein. We used GWAS to explore candidate genes of maize starch pasting properties in this study. The identified candidate genes will be useful for further understanding of the genetic architecture of starch pasting properties in maize. CONCLUSION This study showed a complex regulation network about maize quality trait and starch pasting properties. It may provide some useful markers for marker assisted selection and a basis for cloning the genes behind these SNPs.
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Affiliation(s)
- Xinmei Guo
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Zhaopeng Ge
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Ming Wang
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Meiai Zhao
- grid.412608.90000 0000 9526 6338College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109 China
| | - Yuhe Pei
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
| | - Xiyun Song
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Qingdao, 266109 China
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Xu J, Ma J, Zeng Y, Si H, Wu Y, Zhang S, Shen B. Transcriptome-wide association study identifies novel genes associated with bone mineral density and lean body mass in children. Endocrine 2023; 79:400-409. [PMID: 36572794 PMCID: PMC9892108 DOI: 10.1007/s12020-022-03225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/05/2022] [Indexed: 12/28/2022]
Abstract
OBJECTIVE To identify novel candidate genes whose expression is associated with bone mineral density (BMD) and body lean mass (LM) in children. METHODS A tissue-specific transcriptome-wide association study (TWAS) was conducted utilizing a large-scale genome-wide association study (GWAS) dataset associated with BMD and LM and involving 10,414 participants. The measurement of BMD and LM phenotypes was made based on total-body dual-energy X-ray absorptiometry (TB-DXA) scans. TWAS was conducted by using FUSION software. Reference panels for muscle skeleton (MS), peripheral blood (NBL) and whole blood (YBL) were used for TWAS analysis. Functional enrichment and protein-protein interaction (PPI) analyses of the genes identified by TWAS were performed by using the online tool Metascape ( http://metascape.org ). RESULTS For BMD, we identified 174 genes with P < 0.05, such as IKZF1 (P = 1.46 × 10-9) and CHKB (P = 8.31 × 10-7). For LM, we identified 208 genes with P < 0.05, such as COPS5 (P = 3.03 × 10-12) and MRPS33 (P = 5.45 × 10-10). Gene ontology (GO) enrichment analysis of the BMD-associated genes revealed 200 GO terms, such as protein catabolic process (Log P = -5.09) and steroid hormone-mediated signaling pathway (Log P = -3.13). GO enrichment analysis of the LM-associated genes detected 287 GO terms, such as the apoptotic signaling pathway (Log P = -8.08) and lipid storage (Log P = -3.55). CONCLUSION This study identified several candidate genes for BMD and LM in children, providing novel clues to the genetic mechanisms underlying the development of childhood BMD and LM.
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Affiliation(s)
- Jiawen Xu
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, 37# Guoxue Road, Chengdu, 610041, Sichuan Province, People's Republic of China
| | - Jun Ma
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, 37# Guoxue Road, Chengdu, 610041, Sichuan Province, People's Republic of China
| | - Yi Zeng
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, 37# Guoxue Road, Chengdu, 610041, Sichuan Province, People's Republic of China
| | - Haibo Si
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, 37# Guoxue Road, Chengdu, 610041, Sichuan Province, People's Republic of China
| | - Yuangang Wu
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, 37# Guoxue Road, Chengdu, 610041, Sichuan Province, People's Republic of China
| | - Shaoyun Zhang
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, 37# Guoxue Road, Chengdu, 610041, Sichuan Province, People's Republic of China
| | - Bin Shen
- Orthopedic Research Institute, Department of Orthopedics, Sichuan University West China Hospital, 37# Guoxue Road, Chengdu, 610041, Sichuan Province, People's Republic of China.
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Cameron D, Mi D, Vinh NN, Webber C, Li M, Marín O, O'Donovan MC, Bray NJ. Single-Nuclei RNA Sequencing of 5 Regions of the Human Prenatal Brain Implicates Developing Neuron Populations in Genetic Risk for Schizophrenia. Biol Psychiatry 2023; 93:157-166. [PMID: 36150908 PMCID: PMC10804933 DOI: 10.1016/j.biopsych.2022.06.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND While a variety of evidence supports a prenatal component in schizophrenia, there are few data regarding the cell populations involved. We sought to identify cells of the human prenatal brain mediating genetic risk for schizophrenia by integrating cell-specific gene expression measures generated through single-nuclei RNA sequencing with recent large-scale genome-wide association study (GWAS) and exome sequencing data for the condition. METHODS Single-nuclei RNA sequencing was performed on 5 brain regions (frontal cortex, ganglionic eminence, hippocampus, thalamus, and cerebellum) from 3 fetuses from the second trimester of gestation. Enrichment of schizophrenia common variant genetic liability and rare damaging coding variation was assessed in relation to gene expression specificity within each identified cell population. RESULTS Common risk variants were prominently enriched within genes with high expression specificity for developing neuron populations within the frontal cortex, ganglionic eminence, and hippocampus. Enrichments were largely independent of genes expressed in neuronal populations of the adult brain that have been implicated in schizophrenia through the same methods. Genes containing an excess of rare damaging variants in schizophrenia had higher expression specificity for developing glutamatergic neurons of the frontal cortex and hippocampus that were also enriched for common variant liability. CONCLUSIONS We found evidence for a distinct contribution of prenatal neuronal development to genetic risk for schizophrenia, involving specific populations of developing neurons within the second-trimester fetal brain. Our study significantly advances the understanding of the neurodevelopmental origins of schizophrenia and provides a resource with which to investigate the prenatal antecedents of other psychiatric and neurologic disorders.
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Affiliation(s)
- Darren Cameron
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom
| | - Da Mi
- Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ngoc-Nga Vinh
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom
| | - Caleb Webber
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Meng Li
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom; Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Oscar Marín
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, United Kingdom; Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff, United Kingdom; Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom.
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Wolter JM, Le BD, Matoba N, Lafferty MJ, Aygün N, Liang D, Courtney K, Song J, Piven J, Zylka MJ, Stein JL. Cellular Genome-wide Association Study Identifies Common Genetic Variation Influencing Lithium-Induced Neural Progenitor Proliferation. Biol Psychiatry 2023; 93:8-17. [PMID: 36307327 PMCID: PMC9982734 DOI: 10.1016/j.biopsych.2022.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/22/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND Bipolar disorder is a highly heritable neuropsychiatric condition affecting more than 1% of the human population. Lithium salts are commonly prescribed as a mood stabilizer for individuals with bipolar disorder. Lithium is clinically effective in approximately half of treated individuals, and their genetic backgrounds are known to influence treatment outcomes. While the mechanism of lithium's therapeutic action is unclear, it stimulates adult neural progenitor cell proliferation, similar to some antidepressant drugs. METHODS To identify common genetic variants that modulate lithium-induced proliferation, we conducted an EdU incorporation assay in a library of 80 genotyped human neural progenitor cells treated with lithium. These data were used to perform a genome-wide association study to identify common genetic variants that influence lithium-induced neural progenitor cell proliferation. We manipulated the expression of a putatively causal gene using CRISPRi/a (clustered regularly interspaced short palindromic repeats interference/activation) constructs to experimentally verify lithium-induced proliferation effects. RESULTS We identified a locus on chr3p21.1 associated with lithium-induced proliferation. This locus is also associated with bipolar disorder risk, schizophrenia risk, and interindividual differences in intelligence. We identified a single gene, GNL3, whose expression temporally increased in an allele-specific fashion following lithium treatment. Experimentally increasing the expression of GNL3 led to increased proliferation under baseline conditions, while experimentally decreasing GNL3 expression suppressed lithium-induced proliferation. CONCLUSIONS Our experiments reveal that common genetic variation modulates lithium-induced neural progenitor proliferation and that GNL3 expression is necessary for the full proliferation-stimulating effects of lithium. These results suggest that performing genome-wide associations in genetically diverse human cell lines is a useful approach to discover context-specific pharmacogenomic effects.
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Affiliation(s)
- Justin M Wolter
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Brandon D Le
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nana Matoba
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael J Lafferty
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nil Aygün
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Dan Liang
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kenan Courtney
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Juan Song
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph Piven
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mark J Zylka
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jason L Stein
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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Kim JS, Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Kanatani A, Saisho D, Nishii R, Lipka AE, Hirayama T, Sato K, Mochida K. Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces. J Genet Genomics 2022:S1673-8527(22)00267-3. [PMID: 36566016 DOI: 10.1016/j.jgg.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Barley (Hordeum vulgare ssp. vulgare) was one of the first crops to be domesticated and is adapted to a wide range of environments. Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity. Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits, polymorphisms from East Asian varieties remain scarce. In this study, we analyzed exome polymorphisms in a panel of 274 barley varieties collected worldwide, including 137 varieties from East Asian countries and Ethiopia. We revealed the underlying population structure and conducted genome-wide association studies for ten agronomic traits. Moreover, we examined genome-wide associations for traits related to grain size such as awn length and glume length. Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties, highlighting their distinct genomic signatures relative to Western subpopulations.
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Zhang Z, Liu L, Zhang H, Li C, Chen Y, Zhang J, Pan C, Cheng S, Yang X, Meng P, Yao Y, Jia Y, Wen Y, Zhang F. The genetic structure of pain in depression patients: A genome-wide association study and proteome-wide association study. J Psychiatr Res 2022; 156:547-556. [PMID: 36368244 DOI: 10.1016/j.jpsychires.2022.10.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/18/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Comparing with the general population, the pain in depression patients has more complex biological mechanism. We aim to explore the etiological mechanism of pain in depression patients from the perspective of genetics. METHODS Utilizing the UK Biobank samples with self-reported depression status or PHQ score ≥10, we conducted genome-wide association studies (GWAS) of seven pain traits (N = 1,133-58,349). Additionally, we used FUSION pipeline to perform proteome-wide association study (PWAS) and transcriptome-wide association study (TWAS) by integrating GWAS summary data with two different proteome reference weights (ROS/MAP and Banner) and Rnaseq gene expression reference weights, respectively. RESULTS GWAS identified 3 significant genes associated with different pain traits in depression patients, including TRIOBP (PGWAS = 4.48 × 10-8) for stomach or abdominal pain, SLC9A9(PGWAS = 2.77 × 10-8) for multisite chronic pain (MCP) and ADGRF1 (PGWAS = 1.51 × 10-8) for neck or shoulder pain. In addition, PWAS and TWAS analysis also identified multiple candidate genes associated with different pain traits in depression patients, such as TPRG1L (PPWAS-Banner = 3.38 × 10-2) and SIRPA (PPWAS-Banner = 3.65 × 10-2) for MCP, etc. Notably, when comparing the results of PWAS and TWAS analysis, we found overlapping candidate genes in these pain traits, such as GSTM3 (PPWAS-Banner = 3.38 × 10-2, PTWAS = 6.92 × 10-3) in the stomach or abdominal pain phenotype, ATG7 (PPWAS-Rosmap = 3.15 × 10-2, PTWAS = 2.98 × 10-2) in the MCP, etc. CONCLUSIONS: We identified multiple novel candidate genes for pain traits in depression patients from different perspectives of genetics, which provided novel clues for understanding the genetic mechanisms underlying the pain in depression patients.
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Affiliation(s)
- Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chun'e Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China.
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Franco MF, Polacco AN, Campos PE, Pontaroli AC, Vanzetti LS. Genome-wide association study for resistance in bread wheat (Triticum aestivum L.) to stripe rust (Puccinia striiformis f. sp. tritici) races in Argentina. BMC Plant Biol 2022; 22:543. [PMID: 36434507 PMCID: PMC9701071 DOI: 10.1186/s12870-022-03916-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of the wheat crop. It causes significant reductions in both grain yield and grain quality. In recent years, new and more virulent races have overcome many of the known resistance genes in Argentinian germplasm. In order to identify loci conferring resistance to the local races of Pst for effective utilization in future breeding programs, a genome-wide association study (GWAS) was performed using a collection of 245 bread wheat lines genotyped with 90 K SNPs. RESULTS To search for adult plant resistance (APR) the panel was evaluated for disease severity (DS) and area under disease progress curve (AUDPC) in field trials during two years under natural infection conditions. To look for seedling or all-stage resistance (ASR) the panel was evaluated to determine infection type (IT) under greenhouse conditions against two prevalent races in Argentina. The phenotypic data showed that the panel possessed enough genetic variability for searching for sources of resistance to Pst. Significant correlations between years were observed for Pst response in the field and high heritability values were found for DS (H2 = 0.89) and AUDPC (H2 = 0.93). Based on GWAS, eight markers associated with Pst resistance (FDR < 0.01) were identified, of these, five were associated with ASR (on chromosomes 1B, 2A, 3A and 5B) and three with APR (on chromosomes 3B and 7A). These markers explained between 2% and 32.62% of the phenotypic variation. Five of the markers corresponded with previously reported Yr genes/QTL, while the other three (QYr.Bce.1B.sd.1, QYr.Bce.3A.sd and QYr.Bce.3B.APR.2) might be novel resistance loci. CONCLUSION Our results revealed high genetic variation for resistance to Argentinian stripe rust races in the germplasm used here. It constitutes a very promising step towards the improvement of Pst resistance of bread wheat in Argentina. Also, the identification of new resistance loci would represent a substantial advance for diversifying the current set of resistance genes and to advance in the improvement of the durable resistance to the disease.
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Affiliation(s)
- M F Franco
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, 7620, Balcarce, CP, Argentina.
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina.
- Estación Experimental Agropecuaria INTA Balcarce, 7620, Balcarce, CP, Argentina.
| | - A N Polacco
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, 7620, Balcarce, CP, Argentina
| | - P E Campos
- Estación Experimental Agropecuaria INTA Bordenave, 8187, Bordenave, CP, Argentina
| | - A C Pontaroli
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
- Estación Experimental Agropecuaria INTA Balcarce, 7620, Balcarce, CP, Argentina
| | - L S Vanzetti
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
- Estación Experimental Agropecuaria INTA Marcos Juárez, 2580, Marcos Juárez, CP, Argentina
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Hitomi Y, Aiba Y, Ueno K, Nishida N, Kawai Y, Kawashima M, Tsuiji M, Iwabuchi C, Takada S, Miyake N, Nagasaki M, Tokunaga K, Nakamura M. rs2013278 in the multiple immunological-trait susceptibility locus CD28 regulates the production of non-functional splicing isoforms. Hum Genomics 2022; 16:46. [PMID: 36271469 DOI: 10.1186/s40246-022-00419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022] Open
Abstract
Background Ligation of CD28 with ligands such as CD80 or CD86 provides a critical second signal alongside antigen presentation by class II major histocompatibility complex expressed on antigen-presenting cells through the T cell antigen receptor for naïve T cell activation. A number of studies suggested that CD28 plays an important role in the pathogenesis of various human diseases. Recent genome-wide association studies (GWASs) identified CD28 as a susceptibility locus for lymphocyte and eosinophil counts, multiple sclerosis, ulcerative colitis, celiac disease, rheumatoid arthritis, asthma, and primary biliary cholangitis. However, the primary functional variant and molecular mechanisms of disease susceptibility in this locus remain to be elucidated. This study aimed to identify the primary functional variant from thousands of genetic variants in the CD28 locus and elucidate its functional effect on the CD28 molecule. Results Among the genetic variants exhibiting stronger linkage disequilibrium (LD) with all GWAS-lead variants in the CD28 locus, rs2013278, located in the Rbfox binding motif related to splicing regulation, was identified as a primary functional variant related to multiple immunological traits. Relative endogenous expression levels of CD28 splicing isoforms (CD28i and CD28Δex2) compared with full-length CD28 in allele knock-in cell lines generated using CRISPR/Cas9 were directly regulated by rs2013278 (P < 0.05). Although full-length CD28 protein expressed on Jurkat T cells showed higher binding affinity for CD80/CD86, both CD28i and CD28Δex2 encoded loss-of-function isoforms. Conclusion The present study demonstrated for the first time that CD28 has a shared disease-related primary functional variant (i.e., rs2013278) that regulates the CD28 alternative splicing that generates loss-of-function isoforms. They reduce disease risk by inducing anergy of effector T cells that over-react to autoantigens and allergens. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00419-7.
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Hertz DL, Douglas JA, Miller RM, Kidwell KM, Gersch CL, Desta Z, Storniolo AM, Stearns V, Skaar TC, Hayes DF, Henry NL, Rae JM. Genome-wide association study of aromatase inhibitor discontinuation due to musculoskeletal symptoms. Support Care Cancer 2022; 30:8059-8067. [PMID: 35776183 PMCID: PMC9529953 DOI: 10.1007/s00520-022-07243-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVE Aromatase inhibitors (AIs) are commonly used to treat hormone receptor positive (HR +) breast cancer. AI-induced musculoskeletal syndrome (AIMSS) is a common toxicity that causes AI treatment discontinuation. The objective of this genome-wide association study (GWAS) was to identify genetic variants associated with discontinuation of AI therapy due to AIMSS and attempt to replicate previously reported associations. METHODS In the Exemestane and Letrozole Pharmacogenetics (ELPh) study, postmenopausal patients with HR + non-metastatic breast cancer were randomized to letrozole or exemestane. Genome-wide genotyping of germline DNA was conducted followed by imputation. Each imputed variant was tested for association with time-to-treatment discontinuation due to AIMSS using a Cox proportional hazards model assuming additive genetic effects and adjusting for age, baseline pain score, prior taxane treatment, and AI arm. Secondary analyses were conducted within each AI arm and analyses of candidate variants previously reported to be associated with AIMSS risk. RESULTS Four hundred ELPh participants were included in the combined analysis. Two variants surpassed the genome-wide significance level in the primary analysis (p value < 5 × 10-8), an intronic variant (rs79048288) within CCDC148 (HR = 4.42, 95% CI: 2.67-7.33) and an intergenic variant (rs912571) upstream of PPP1R14C (HR = 0.30, 95% CI: 0.20-0.47). In the secondary analysis, rs74418677, which is known to be associated with expression of SUPT20H, was significantly associated with discontinuation of letrozole therapy due to AIMSS (HR = 5.91, 95% CI: 3.16-11.06). We were able to replicate associations for candidate variants previously reported to be associated with AIMSS in this cohort, but were not able to replicate associations for any other variants previously reported in other patient cohorts. CONCLUSIONS Our GWAS findings identify several candidate variants that may be associated with AIMSS risk from AI generally or letrozole specifically. Validation of these associations in independent cohorts is needed before translating these findings into clinical practice to improve treatment outcomes in patients with HR + breast cancer.
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Affiliation(s)
- Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, 428 Church St., Room 3054, Ann Arbor, MI, 48109-1065, USA.
| | - Julie A Douglas
- Department of Mathematics and Statistics, Skidmore College, Saratoga Springs, NY, 12866, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Robert M Miller
- Department of Mathematics and Statistics, Skidmore College, Saratoga Springs, NY, 12866, USA
| | - Kelley M Kidwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Christina L Gersch
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | | | - Vered Stearns
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Todd C Skaar
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Daniel F Hayes
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - N Lynn Henry
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James M Rae
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
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Zai CC, Cheema SY, Zai GC, Tiwari AK, Kennedy JL. Post-traumatic stress disorder in the Canadian Longitudinal Study on Aging: A genome-wide association study. J Psychiatr Res 2022; 154:209-18. [PMID: 35952521 DOI: 10.1016/j.jpsychires.2022.07.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/06/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Canada exhibits one of highest lifetime prevalence for post-traumatic stress disorder (PTSD), but the etiology of this debilitating mental health condition still remains largely unknown. This study aims to examine the genetics of PTSD in the Canadian Longitudinal Study on Aging (CLSA) to identify potential genetic factors involved in the development of PTSD. METHOD The CLSA sample was screened for primary (PTSD status) and secondary outcomes (avoidance, detachment, guardedness, and nightmares) based on the Primary Care PTSD Screen Scale (PC-PTSD). After GWAS quality control and whole-genome imputation, single-marker, gene-based, and polygenic risk score (PRS) analyses were performed. RESULTS Based on available genotype and phenotype data, N = 16,535 individuals were selected for the analyses. While genome-wide analyses did not show significant findings for our primary and secondary outcomes, PRS analyses showed variable levels of association between PC-PTSD items with trauma, major depressive disorder, schizophrenia, bipolar disorder, educational attainment, and insomnia (p < 5e-4). CONCLUSION This is the first GWAS of PTSD status and individual PC-PTSD items in a population sample of older adults from Canada. This study was also able to replicate findings from previous studies. Genetic investigations into individual symptom components of PTSD may help untangle the complex genetic architecture of PTSD.
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Chou CH, Lin HS, Wen CH, Tung CW. Patterns of genetic variation and QTLs controlling grain traits in a collection of global wheat germplasm revealed by high-quality SNP markers. BMC Plant Biol 2022; 22:455. [PMID: 36131260 PMCID: PMC9494784 DOI: 10.1186/s12870-022-03844-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Establish a molecular breeding program involved assembling a diverse germplasm collection and generating accurate genotypes to characterize their genetic potential and associate them with agronomic traits. In this study, we acquired over eight hundred wheat accessions from international gene banks and assessed their genetic relatedness using high-quality SNP genotypes. Understanding the scope of genomic variation in this collection allows the breeders to utilize the genetic resources efficiently while improving wheat yield and quality. RESULTS A wheat diversity panel comprising 39 durum wheat, 60 spelt wheat, and 765 bread wheat accessions was genotyped on iSelect 90 K wheat SNP arrays. A total of 57,398 SNP markers were mapped to IWGSC RefSeq v2.1 assembly, over 30,000 polymorphic SNPs in the A, B, D genomes were used to analyze population structure and diversity, the results revealed the separation of the three species and the differentiation of CIMMYT improved breeding lines and landraces or widely grown cultivars. In addition, several chromosomal regions under selection were detected. A subset of 280 bread wheat accessions was evaluated for grain traits, including grain length, width, surface area, and color. Genome-wide association studies (GWAS) revealed that several chromosomal regions were significantly linked to known quantitative trait loci (QTL) controlling grain-related traits. One of the SNP peaks at the end of chromosome 7A was in strong linkage disequilibrium (LD) with WAPO-A1, a gene that governs yield components. CONCLUSIONS Here, the most updated and accurate physical positions of SNPs on 90 K genotyping array are provided for the first time. The diverse germplasm collection and associated genotypes are available for the wheat researchers to use in their molecular breeding program. We expect these resources to broaden the genetic basis of original breeding and pre-breeding materials and ultimately identify molecular markers associated with important agronomic traits which are evaluated in diverse environmental conditions.
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Affiliation(s)
- Chia-Hui Chou
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Hsun-Shih Lin
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chen-Hsin Wen
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan.
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Alsaleh A. SSR-based genome-wide association study in turkish durum wheat germplasms revealed novel QTL of accumulated platinum. Mol Biol Rep 2022; 49:11289-11300. [PMID: 35819556 DOI: 10.1007/s11033-022-07720-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/05/2022] [Accepted: 06/14/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Durum wheat has a genetic capacity to accumulate toxic metals that can exceed the safety limit of the international standards, which may seriously affect human health. Identifying germplasms with low, nontoxic accumulated metal contents is important to select and develop new varieties. Thus, the objective of this study is to identify the levels of accumulated platinum in durum wheat and detect novel QTL. METHODS AND RESULTS Platinum contents were determined using 130 durum genotypes. Results generally showed low values of accumulated Pt and significantly less than the maximum grain's Pt content determined by international standards. Pt contents among genotypes varied from ≤ 0.001 to 0.72 µg/kg with an average of 0.02. Landraces showed the lowest average accumulated Pt. GWAS was then performed with 780 SSR markers. Five QTL were detected and explained 14.4-23.1% of the total phenotypic variation. Chromosomes 3 A, 3B, and 5B appear to be hotspots and may play a crucial role in accumulated Pt and were harbored in 1, 3, and 1 QTL, respectively. CONCLUSIONS This assessment of accumulated Pt within a unique panel included accessions mostly from Turkish regions, and GWAS used is the first study regarding accumulated Pt indices to reveal novel QTL. It will allow breeders to accelerate their selection of proper genotypes according to desired alleles and offer an opportunity to apply MAS to minimize Pt toxicity in durum wheat. Results indicated that the significance of genome (B) regions are likely related to the inheritance control of Pt content and may play a pivotal role regarding durum wheat's Pt contents. Nonetheless, these novel QTL should be validated in independent populations in numerous environments.
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Affiliation(s)
- Ahmad Alsaleh
- Department of Agriculture and Food, Institute of Hemp Research, Yozgat Bozok University, 66200, Yozgat, Turkey.
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Chen R, Yang Z, Liu J, Cai X, Huo Y, Zhang Z, Li M, Chang H, Luo XJ. Functional genomic analysis delineates regulatory mechanisms of GWAS-identified bipolar disorder risk variants. Genome Med 2022; 14:53. [PMID: 35590387 PMCID: PMC9121601 DOI: 10.1186/s13073-022-01057-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 05/11/2022] [Indexed: 01/23/2023] Open
Abstract
Background Genome-wide association studies (GWASs) have identified multiple risk loci for bipolar disorder (BD). However, pinpointing functional (or causal) variants in the reported risk loci and elucidating their regulatory mechanisms remain challenging. Methods We first integrated chromatin immunoprecipitation sequencing (ChIP-Seq) data from human brain tissues (or neuronal cell lines) and position weight matrix (PWM) data to identify functional single-nucleotide polymorphisms (SNPs). Then, we verified the regulatory effects of these transcription factor (TF) binding–disrupting SNPs (hereafter referred to as “functional SNPs”) through a series of experiments, including reporter gene assays, allele-specific expression (ASE) analysis, TF knockdown, CRISPR/Cas9-mediated genome editing, and expression quantitative trait loci (eQTL) analysis. Finally, we overexpressed PACS1 (whose expression was most significantly associated with the identified functional SNPs rs10896081 and rs3862386) in mouse primary cortical neurons to investigate if PACS1 affects dendritic spine density. Results We identified 16 functional SNPs (in 9 risk loci); these functional SNPs disrupted the binding of 7 TFs, for example, CTCF and REST binding was frequently disrupted. We then identified the potential target genes whose expression in the human brain was regulated by these functional SNPs through eQTL analysis. Of note, we showed dysregulation of some target genes of the identified TF binding–disrupting SNPs in BD patients compared with controls, and overexpression of PACS1 reduced the density of dendritic spines, revealing the possible biological mechanisms of these functional SNPs in BD. Conclusions Our study identifies functional SNPs in some reported risk loci and sheds light on the regulatory mechanisms of BD risk variants. Further functional characterization and mechanistic studies of these functional SNPs and candidate genes will help to elucidate BD pathogenesis and develop new therapeutic approaches and drugs. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01057-3.
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Affiliation(s)
- Rui Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhihui Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Xin Cai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Yongxia Huo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhijun Zhang
- Department of Neurology, Affiliated Zhongda Hospital, Southeast University, Nanjing, Jiangsu, 210096, China.,Key Laboratory of Developmental Genes and Human Disease of Ministry of Education, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
| | - Hong Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China. .,Department of Neurology, Affiliated Zhongda Hospital, Southeast University, Nanjing, Jiangsu, 210096, China. .,Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Southeast University, Nanjing, Jiangsu, 210096, China.
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Ding Y, Qiu X, Luo H, Huang L, Guo J, Yu B, Sudini H, Pandey M, Kang Y, Liu N, Zhou X, Chen W, Chen Y, Wang X, Huai D, Yan L, Lei Y, Jiang H, Varshney R, Liu K, Liao B. Comprehensive evaluation of Chinese peanut mini-mini core collection and QTL mapping for aflatoxin resistance. BMC Plant Biol 2022; 22:207. [PMID: 35448951 PMCID: PMC9027753 DOI: 10.1186/s12870-022-03582-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Aflatoxin contamination caused by Aspergillus fungi has been a serious factor affecting food safety of peanut (Arachis hypogaea L.) because aflatoxins are highly harmful for human and animal health. As three mechanisms of resistance to aflatoxin in peanut including shell infection resistance, seed infection resistance and aflatoxin production resistance exist among naturally evolved germplasm stocks, it is highly crucial to pyramid these three resistances for promoting peanut industry development and protecting consumers' health. However, less research effort has been made yet to investigate the differentiation and genetic relationship among the three resistances in diversified peanut germplasm collections. RESULTS In this study, the Chinese peanut mini-mini core collection selected from a large basic collection was systematically evaluated for the three resistances against A. flavus for the first time. The research revealed a wide variation among the diversified peanut accessions for all the three resistances. Totally, 14 resistant accessions were identified, including three with shell infection resistance, seven with seed infection resistance and five with aflatoxin production resistance. A special accession, Zh.h1312, was identified with both seed infection and aflatoxin production resistance. Among the five botanic types of A. hypogaea, the var. vulgaris (Spanish type) belonging to subspecies fastigiata is the only one which possessed all the three resistances. There was no close correlation between shell infection resistance and other two resistances, while there was a significant positive correlation between seed infection and toxin production resistance. All the three resistances had a significant negative correlation with pod or seed size. A total of 16 SNPs/InDels associated with the three resistances were identified through genome-wide association study (GWAS). Through comparative analysis, Zh.h1312 with seed infection resistance and aflatoxin production resistance was also revealed to possess all the resistance alleles of associated loci for seed infection index and aflatoxin content. CONCLUSIONS This study provided the first comprehensive understanding of differentiation of aflatoxin resistance in diversified peanut germplasm collection, and would further contribute to the genetic enhancement for resistance to aflatoxin contamination.
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Affiliation(s)
- Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xike Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Hari Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Manish Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
| | - Rajeev Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Kede Liu
- National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062 China
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Ferrero-Serrano Á, Sylvia MM, Forstmeier PC, Olson AJ, Ware D, Bevilacqua PC, Assmann SM. Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis. Genome Biol 2022; 23:101. [PMID: 35440059 PMCID: PMC9017077 DOI: 10.1186/s13059-022-02656-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or “riboSNitches.” Results We experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation. Conclusion We functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term “conditional riboSNitch.” We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02656-4.
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Affiliation(s)
- Ángel Ferrero-Serrano
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Megan M Sylvia
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Peter C Forstmeier
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Andrew J Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Philip C Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA. .,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
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Pan Y, Zhu J, Hong Y, Zhang M, Lv C, Guo B, Shen H, Xu X, Xu R. Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease. PeerJ 2022; 10:e13128. [PMID: 35317071 PMCID: PMC8934529 DOI: 10.7717/peerj.13128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/25/2022] [Indexed: 01/12/2023] Open
Abstract
Background The disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping. Methods A natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites. Results Seven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differentially identified under geographically distinct regions. Our research provides novel genetic resources and resistance loci for breeding barley varieties for BaMYV disease resistance.
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Affiliation(s)
- Yuhan Pan
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Juan Zhu
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Yi Hong
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Mengna Zhang
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Chao Lv
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Baojian Guo
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
| | - Huiquan Shen
- Jiangsu Institute for Seaside Agricultural Sciences and Yancheng Academy of Agricultural Science, Yancheng, Jiangsu, China
| | - Xiao Xu
- Jiangsu Institute for Seaside Agricultural Sciences and Yancheng Academy of Agricultural Science, Yancheng, Jiangsu, China
| | - Rugen Xu
- Yangzhou University, Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Institutes of Agricultural Science, Yangzhou, Jiangsu, China
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Liu W, Sun Q, Huang L, Bhattacharya A, Wang GW, Tan X, Kuban KCK, Joseph RM, O'Shea TM, Fry RC, Li Y, Santos HP. Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm. J Neurodev Disord 2022; 14:16. [PMID: 35240980 PMCID: PMC8903548 DOI: 10.1186/s11689-022-09429-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/22/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Although survival rates for infants born extremely preterm (gestation < 28 weeks) have improved significantly in recent decades, neurodevelopmental impairment remains a major concern. Children born extremely preterm remain at high risk for cognitive impairment from early childhood to adulthood. However, there is limited evidence on genetic factors associated with cognitive impairment in this population. METHODS First, we used a latent profile analysis (LPA) approach to characterize neurocognitive function at age 10 for children born extremely preterm. Children were classified into two groups: (1) no or low cognitive impairment, and (2) moderate-to-severe cognitive impairment. Second, we performed TOPMed-based genotype imputation on samples with genotype array data (n = 528). Third, we then conducted a genome-wide association study (GWAS) for LPA-inferred cognitive impairment. Finally, computational analysis was conducted to explore potential mechanisms underlying the variant x LPA association. RESULTS We identified two loci reaching genome-wide significance (p value < 5e-8): TEA domain transcription factor 4 (TEAD4 at rs11829294, p value = 2.40e-8) and syntaxin 18 (STX18 at rs79453226, p value = 1.91e-8). Integrative analysis with brain expression quantitative trait loci (eQTL), chromatin conformation, and epigenomic annotations suggests tetraspanin 9 (TSPAN9) and protein arginine methyltransferase 8 (PRMT8) as potential functional genes underlying the GWAS signal at the TEAD4 locus. CONCLUSIONS We conducted a novel computational analysis by utilizing an LPA-inferred phenotype with genetics data for the first time. This study suggests that rs11829294 and its LD buddies have potential regulatory roles on genes that could impact neurocognitive impairment for extreme preterm born children.
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Affiliation(s)
- Weifang Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Le Huang
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Geoffery W Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xianming Tan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karl C K Kuban
- Department of Pediatrics, Boston University, Boston, MA, USA
| | - Robert M Joseph
- Department of Anatomy & Neurobiology, Boston University, Boston, MA, USA
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hudson P Santos
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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