1
|
Sun S, Liu Q, Wang Z, Huang YY, Sublette ME, Dwork AJ, Rosoklija G, Ge Y, Galfalvy H, Mann JJ, Haghighi F. Brain and blood transcriptome profiles delineate common genetic pathways across suicidal ideation and suicide. Mol Psychiatry 2024; 29:1417-1426. [PMID: 38278992 PMCID: PMC11189724 DOI: 10.1038/s41380-024-02420-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to the severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with the presence of suicidal ideation were found within 18 co-expressed modules (p < 0.05), as well as in 3 co-expressed modules associated with suicidal ideation severity (p < 0.05, not explained by severity of depression). Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified and investigated using RNA-seq data from postmortem brain that revealed gene expression differences with moderate effect sizes in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity are associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.
Collapse
Affiliation(s)
- Shengnan Sun
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Qingkun Liu
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Zhaoyu Wang
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Yung-Yu Huang
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - M Elizabeth Sublette
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hanga Galfalvy
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Fatemeh Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA.
| |
Collapse
|
2
|
Kanchibhotla SC, Mather KA, Armstrong NJ, Ciobanu LG, Baune BT, Catts VS, Schofield PR, Trollor JN, Ames D, Sachdev PS, Thalamuthu A. Heritability of Gene Expression Measured from Peripheral Blood in Older Adults. Genes (Basel) 2024; 15:495. [PMID: 38674429 PMCID: PMC11049887 DOI: 10.3390/genes15040495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The contributions of genetic variation and the environment to gene expression may change across the lifespan. However, few studies have investigated the heritability of blood gene expression in older adults. The current study therefore aimed to investigate this question in a community sample of older adults. A total of 246 adults (71 MZ and 52 DZ twins, 69.91% females; mean age-75.79 ± 5.44) were studied. Peripheral blood gene expression was assessed using Illumina microarrays. A heritability analysis was performed using structural equation modelling. There were 5269 probes (19.9%) from 4603 unique genes (23.9%) (total 26,537 probes from 19,256 genes) that were significantly heritable (mean h2 = 0.40). A pathway analysis of the top 10% of significant genes showed enrichment for the immune response and ageing-associated genes. In a comparison with two other gene expression twin heritability studies using adults from across the lifespan, there were 38 out of 9479 overlapping genes that were significantly heritable. In conclusion, our study found ~24% of the available genes for analysis were heritable in older adults, with only a small number common across studies that used samples from across adulthood, indicating the importance of examining gene expression in older age groups.
Collapse
Affiliation(s)
- Sri C. Kanchibhotla
- Centre for Healthy Brain Ageing, Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Karen A. Mather
- Centre for Healthy Brain Ageing, Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Neuroscience Research Australia, Sydney, NSW 2031, Australia
| | - Nicola J. Armstrong
- Department of Mathematics and Statistics, Curtin University, Perth, WA 6845, Australia
| | - Liliana G. Ciobanu
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Bernhard T. Baune
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5005, Australia
- Department of Psychiatry, University of Münster, 48149 Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Vibeke S. Catts
- Centre for Healthy Brain Ageing, Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter R. Schofield
- Neuroscience Research Australia, Sydney, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Julian N. Trollor
- Centre for Healthy Brain Ageing, Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Developmental Disability Neuropsychiatry, Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - David Ames
- Academic Unit for Psychiatry of Old Age, University of Melbourne, St George’s Hospital, Kew, Melbourne, VIC 3010, Australia
- National Ageing Research Institute, Parkville, VIC 3052, Australia
| | - Perminder S. Sachdev
- Centre for Healthy Brain Ageing, Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
3
|
Feng W, Xu Y, Su S, Yu F, Li J, Jia R, Song C, Li H, Xu P, Tang Y. Transcriptomic analysis of hydrogen peroxide-induced liver dysfunction in Cyprinus carpio: Insights into protein synthesis and metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170393. [PMID: 38280587 DOI: 10.1016/j.scitotenv.2024.170393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Hydrogen peroxide (H2O2), a prevalent reactive oxygen species (ROS) found in natural aquatic environments, has garnered significant attention for its potential toxicity in fish. However, the molecular mechanisms underlying this toxicity are not yet comprehensively understood. This study aimed to assess H2O2-induced liver dysfunction in common carp (Cyprinus carpio) and elucidate the underlying molecular mechanisms via biochemical and transcriptomic analyses. Common carp were divided into normal control (NC) and H2O2-treated groups (1 mM H2O2), the latter of which was exposed to H2O2 for 1 h per day over a period of 14 days. Serum biochemical analyses indicated that exposure to H2O2 resulted in moderate liver damage, characterized by elevated alanine aminotransferase (ALT) activity and lowered albumin (Alb) level. Concurrently, H2O2 exposure induced oxidative stress and modified the hepatic metabolic enzyme levels. Transcriptome analysis highlighted that 1358 and 1188 genes were significantly downregulated and upregulated, respectively, in the H2O2-treated group. These differentially expressed genes (DEGs) were significantly enriched in protein synthesis and a variety of metabolic functions such as peptide biosynthetic processes, protein transport, ribonucleoprotein complex biogenesis, oxoacid metabolic processes, and tricarboxylic acid metabolic processes. Dysregulation of protein synthesis is principally associated with the downregulation of three specific pathways: ribosome biogenesis, protein export, and protein processing in the endoplasmic reticulum (ER). Furthermore, metabolic abnormalities were primarily characterized by inhibition of the citrate cycle (TCA) and fatty acid biosynthesis. Significantly, anomalies in both protein synthesis and metabolic function may be linked to aberrant regulation of the insulin signaling pathway. These findings offer innovative insights into the mechanisms underlying H2O2 toxicity in aquatic animals, contributing to the assessment of ecological risks.
Collapse
Affiliation(s)
- Wenrong Feng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Yuanfeng Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Fan Yu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jianlin Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Rui Jia
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Changyou Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hongxia Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| |
Collapse
|
4
|
Long X, Zhang C, Yang Q, Zhang X, Chen W, Zhu X, Xu Q, Tan Q. Photoheterotroph improved the growth and nutrient levels of Chlorella vulgaris and the related molecular mechanism. Appl Microbiol Biotechnol 2024; 108:269. [PMID: 38507095 PMCID: PMC10954984 DOI: 10.1007/s00253-024-13090-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/16/2024] [Accepted: 02/25/2024] [Indexed: 03/22/2024]
Abstract
Microalgae are rich in fatty acids, proteins, and other nutrients, which have gained the general attention of researchers all over the world. For the development of Chlorella vulgaris in food and feed industry, this study was conducted to investigate the differences in C. vulgaris' growth and nutritional components under different culture conditions (autotrophic, heterotrophic, photoheterotrophic) and the internal factors through cell counting in combination with transcriptome and nutrient analyses. The results showed that, under the photoheterotrophic condition, Chlorella's growth and the contents of lipid and protein were significantly higher than that under the heterotrophic condition, and the moisture content was lower than that under the heterotrophic condition. The saturated fatty acid content under the photoheterotrophic condition was the lowest, while the polyunsaturated fatty acid content was significantly higher than those under the other two conditions. There were 46,583 differentially expressed genes (DEGs), including 33,039 up-regulated DEGs (70.93%) and 13,544 down-regulated DEGs (29.07%), under the photoheterotrophic condition in comparison with the autotrophic condition. The fold change between the two conditions of samples of up-regulated genes was higher than that of the down-regulated genes. The KEGG enrichment showed that the up-regulated DEGs in the photoheterotrophic condition were significantly enriched in 5 pathways, including protein processing in endoplasmic reticulum pathway, photosynthesis pathway, photosynthesis-antenna protein pathway, endocytosis pathway, and phosphonate and phosphinate metabolism pathway. DEGs related to fatty acid metabolic pathways were significantly enriched in the fatty acid biosynthesis pathway and the biosynthesis of unsaturated fatty acid pathway. The qPCR analysis showed that the expression pattern of the selected genes was consistent with that of transcriptome analysis. The results of this study lay a theoretical foundation for the large-scale production of Chlorella and its application in food, feed, and biodiesel. KEY POINTS: • Nutrient levels under photoheterotrophic condition were higher than other conditions. • Six important pathways were discovered that affect changes in nutritional composition. • Explored genes encode important enzymes in the differential metabolic pathways.
Collapse
Affiliation(s)
- Xianmei Long
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Cancan Zhang
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qian Yang
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xiaorui Zhang
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Wangwang Chen
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Xiaofang Zhu
- Hubei Vocational College of Bio-Technology, Wuhan, 430070, China
| | - Qing Xu
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qingsong Tan
- National Demonstration Center for Experimental Aquaculture Education, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China.
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
| |
Collapse
|
5
|
Huang S, Li Y, Shen J, Liang W, Li C. Identification of a diagnostic model and molecular subtypes of major depressive disorder based on endoplasmic reticulum stress-related genes. Front Psychiatry 2023; 14:1168516. [PMID: 37649561 PMCID: PMC10464956 DOI: 10.3389/fpsyt.2023.1168516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023] Open
Abstract
Subject Major depressive disorder (MDD) negatively affects patients' behaviours and daily lives. Due to the high heterogeneity and complex pathological features of MDD, its diagnosis remains challenging. Evidence suggests that endoplasmic reticulum stress (ERS) is involved in the pathogenesis of MDD; however, relevant diagnostic markers have not been well studied. This study aimed to screen for ERS genes with potential diagnostic value in MDD. Methods Gene expression data on MDD samples were downloaded from the GEO database, and ERS-related genes were obtained from the GeneCards and MSigDB databases. Differentially expressed genes (DEGs) in MDD patients and healthy subjects were identified and then integrated with ERS genes. ERS diagnostic model and nomogram were developed based on biomarkers screened using the LASSO method. The diagnostic performance of this model was evaluated. ERS-associated subtypes were identified. CIBERSORT and GSEA were used to explore the differences between the different subtypes. Finally, WGCNA was performed to identify hub genes related to the subtypes. Results A diagnostic model was developed based on seven ERS genes: KCNE1, PDIA4, STAU1, TMED4, MGST1, RCN1, and SHC1. The validation analysis showed that this model had a good diagnostic performance. KCNE1 expression was positively correlated with M0 macrophages and negatively correlated with resting CD4+ memory T cells. Two subtypes (SubA and SubB) were identified, and these two subtypes showed different ER score. The SubB group showed higher immune infiltration than the SubA group. Finally, NCF4, NCF2, CSF3R, and FPR2 were identified as hub genes associated with ERS molecular subtypes. Conclusion Our current study provides novel diagnostic biomarkers for MDD from an ERS perspective, and these findings further facilitate the use of precision medicine in MDD.
Collapse
Affiliation(s)
- Shuwen Huang
- Research Base of Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- FuJian Key Laboratory of TCM Health State, Fuzhou, Fujian, China
| | - Yong Li
- Research Base of Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- FuJian Key Laboratory of TCM Health State, Fuzhou, Fujian, China
| | - Jianying Shen
- Research Base of Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- FuJian Key Laboratory of TCM Health State, Fuzhou, Fujian, China
| | - Wenna Liang
- Research Base of Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- FuJian Key Laboratory of TCM Health State, Fuzhou, Fujian, China
| | - Candong Li
- Research Base of Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- FuJian Key Laboratory of TCM Health State, Fuzhou, Fujian, China
- LI Candong Qihuang Scholar Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| |
Collapse
|
6
|
Sun S, Liu Q, Wang Z, Huang YY, Sublette M, Dwork A, Rosoklija G, Ge Y, Galfalvy H, Mann JJ, Haghighi F. Functional Architecture of Brain and Blood Transcriptome Delineate Biological Continuity Between Suicidal Ideation and Suicide. RESEARCH SQUARE 2023:rs.3.rs-2958575. [PMID: 37398042 PMCID: PMC10312911 DOI: 10.21203/rs.3.rs-2958575/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with presence and severity of suicidal ideation were found within 18 and 3 co-expressed modules respectively (p < 0.05), not explained by severity of depression. Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified, and tested using RNA-seq data from postmortem brain that revealed gene expression differences in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity is associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.
Collapse
|
7
|
Tang J, Xu Q, Tang K, Ye X, Cao Z, Zou M, Zeng J, Guan X, Han J, Wang Y, Yang L, Lin Y, Jiang K, Chen X, Zhao Y, Tian D, Li C, Shen W, Du X. Susceptibility identification for seasonal influenza A/H3N2 based on baseline blood transcriptome. Front Immunol 2023; 13:1048774. [PMID: 36713410 PMCID: PMC9878565 DOI: 10.3389/fimmu.2022.1048774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction Influenza susceptibility difference is a widely existing trait that has great practical significance for the accurate prevention and control of influenza. Methods Here, we focused on the human susceptibility to the seasonal influenza A/H3N2 of healthy adults at baseline level. Whole blood expression data for influenza A/H3N2 susceptibility from GEO were collected firstly (30 symptomatic and 19 asymptomatic). Then to explore the differences at baseline, a suite of systems biology approaches - the differential expression analysis, co-expression network analysis, and immune cell frequencies analysis were utilized. Results We found the baseline condition, especially immune condition between symptomatic and asymptomatic, was different. Co-expression module that is positively related to asymptomatic is also related to immune cell type of naïve B cell. Function enrichment analysis showed significantly correlation with "B cell receptor signaling pathway", "immune response-activating cell surface receptor signaling pathway" and so on. Also, modules that are positively related to symptomatic are also correlated to immune cell type of neutrophils, with function enrichment analysis showing significantly correlations with "response to bacterium", "inflammatory response", "cAMP-dependent protein kinase complex" and so on. Responses of symptomatic and asymptomatic hosts after virus exposure show differences on resisting the virus, with more effective frontline defense for asymptomatic hosts. A prediction model was also built based on only baseline transcription information to differentiate symptomatic and asymptomatic population with accuracy of 0.79. Discussion The results not only improve our understanding of the immune system and influenza susceptibility, but also provide a new direction for precise and targeted prevention and therapy of influenza.
Collapse
Affiliation(s)
- Jing Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Qiumei Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Kang Tang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Ye
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zicheng Cao
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,School of Public Health, Shantou University, Shantou, China
| | - Min Zou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xinyan Guan
- Department of Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, China
| | - Jinglin Han
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Yihan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Lan Yang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yishan Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Kaiao Jiang
- Palos Verdes Peninsula High School, Rancho Palos Verdes, CA, United States
| | - Xiaoliang Chen
- Department of Chronic Disease Control and Prevention, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, China
| | - Yang Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Chunwei Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Shen
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China,*Correspondence: Xiangjun Du, ; Wei Shen,
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China,*Correspondence: Xiangjun Du, ; Wei Shen,
| |
Collapse
|
8
|
Jia R, Hou Y, Feng W, Li B, Zhu J. Alterations at biochemical, proteomic and transcriptomic levels in liver of tilapia (Oreochromis niloticus) under chronic exposure to environmentally relevant level of glyphosate. CHEMOSPHERE 2022; 294:133818. [PMID: 35114268 DOI: 10.1016/j.chemosphere.2022.133818] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/03/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The toxicity of glyphosate (Gly) on aquatic animals has received attention from many researchers. However, the chronic toxicity mechanism of Gly on fish has not yet been clarified entirely. Thus, this study aimed to explore the potential toxicity mechanism of Gly at 2 mg/L, a possibly existing concentration in the aquatic environment, via biochemical, transcriptomic and proteomic analyses in the liver of tilapia. Long-term Gly exposure increased lipid content, and altered redox status in liver. Transcriptomic analysis revealed that Gly exposure changed dramatically the expression of 225 genes in liver, including 94 up-regulated genes and 131 down-regulated genes. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that these genes were predominantly enriched in ion transport, lipid metabolism and PPAR (peroxisome proliferator-activated receptor) signaling pathway. Meanwhile, at proteomic level, long-term Gly exposure resulted in alteration of 21 proteins, which were principally related to hepatic metabolism function. In conclusion, our data displayed a potential toxicity, mainly manifested as redox imbalance and dysregulation of metabolism function, in the liver of tilapia after long-term Gly exposure at 2 mg/L. This study provided novel insight into underlying toxicity mechanism of long-term Gly exposure at an environmentally relevant concentration in fish.
Collapse
Affiliation(s)
- Rui Jia
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China; International Joint Research Laboratory for Fish Immunopharmacology, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yiran Hou
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wenrong Feng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Bing Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Jian Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| |
Collapse
|
9
|
Yang C, Zhang K, Zhang A, Sun N, Liu Z, Zhang K. Co-Expression Network Modeling Identifies Specific Inflammation and Neurological Disease-Related Genes mRNA Modules in Mood Disorder. Front Genet 2022; 13:865015. [PMID: 35386281 PMCID: PMC8977853 DOI: 10.3389/fgene.2022.865015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/23/2022] [Indexed: 12/03/2022] Open
Abstract
Objectives: Mood disorders are a kind of serious mental illness, although their molecular factors involved in the pathophysiology remain unknown. One approach to examine the molecular basis of mood disorders is co-expression network analysis (WGCNA), which is expected to further divide the set of differentially expressed genes into subgroups (i.e., modules) in a more (biologically) meaningful way, fascinating the downstream enrichment analysis. The aim of our study was to identify hub genes in modules in mood disorders by using WGCNA. Methods: Microarray data for expression values of 4,311,721 mRNA in peripheral blood mononuclear cells drawn from 21 MDD, 8 BD, and 24 HC individuals were obtained from GEO (GSE39653); data for genes with expression in the bottom third for 80% or more of the samples were removed. Then, the top 70% most variable genes/probs were selected for WGCNA: 27,884 probes representing 21,840 genes; correlation between module genes and mood disorder (MDD+BD vs. HC) was evaluated. Results: About 52% of 27,765 genes were found to form 50 co-expression modules with sizes 42–3070. Among the 50 modules, the eigengenes of two modules were significantly correlated with mood disorder (p < 0.05). The saddlebrown module was found in one of the meta-modules in the network of the 50 eigengenes along with mood disorder, 6 (IER5, NFKBIZ, CITED2, TNF, SERTAD1, ADM) out of 12 differentially expressed genes identified in Savitz et al. were found in the saddlebrown module. Conclusions: We found a significant overlap for 6 hub genes (ADM, CITED2, IER5, NFKBIZ, SERTAD1, TNF) with similar co-expression and dysregulation patterns associated with mood disorder. Overall, our findings support other reports on molecular-level immune dysfunction in mood disorder and provide novel insights into the pathophysiology of mood disorder.
Collapse
Affiliation(s)
- Chunxia Yang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Kun Zhang
- Shanxi Medical University, Taiyuan, China
| | - Aixia Zhang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Ning Sun
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China.,Nuring College of Shanxi Medical University, Taiyuan, China
| | - Zhifen Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Kerang Zhang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, China
| |
Collapse
|
10
|
Zhang J, Xie S, Chen Y, Zhou X, Zheng Z, Yang L, Li Y. Comprehensive analysis of endoplasmic reticulum stress and immune infiltration in major depressive disorder. Front Psychiatry 2022; 13:1008124. [PMID: 36353576 PMCID: PMC9638134 DOI: 10.3389/fpsyt.2022.1008124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is a life-threatening, debilitating mental health condition. An important factor in the development of depression is endoplasmic reticulum stress (ERS). However, their roles in MDD have not yet been established. The goal of this study was to examine ERS and its underlying molecular mechanisms in MDD. METHODS We used data from two microarray datasets (GSE98793 and GSE39653) and the GeneCards database to examine the reticulum stress-related differentially expressed genes (ERSR-DEGs) associated with MDD. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Gene Set Variation Analysis (GSVA) were used to further investigate the function and mechanism of ERS in MDD. Moreover, we constructed protein-protein interaction (PPI) networks to identify hub genes as well as the regulatory network of microRNAs (miRNAs), transcription factors (TFs), and potential drugs related to ERSR-DEGs. CIBERSORT was then used to evaluate the immune activity of MDD samples and conduct a correlation analysis between the hub genes and immune cells. RESULTS In total, 37 ERSR-DEGs and five hub genes were identified (NCF1, MAPK14, CASP1, CYBA, and TNF). Functional enrichment analysis revealed that ERSR-DEGs were predominantly enriched in inflammation-and immunity-related pathways, such as tumor necrosis factor signaling, NF-κB signaling, and Toll-like receptor signaling pathways. Additionally, 179 miRNAs, 25 TFs, and 15 potential drugs were tested for their interactions with the ERSR-DEGs. CIBERSORT found high proportions of Tregs, monocytes, and macrophages M0 in the MDD samples. Among these, hub genes showed a significant correlation with immune cell infiltration in patients with MDD. CONCLUSIONS NCF1, MAPK14, CASP1, CYBA, and TNF are potential ERS-related biomarkers for the diagnosis of MDD. Our research has revealed a significant correlation between immune cells and ERS-related genes with MDD. Not only did our study contribute to a better understanding of the regulatory mechanisms of ERS in underlying MDD pathology, but it also established a paradigm for future studies on ERS.
Collapse
Affiliation(s)
- Jing Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shujun Xie
- Department of Internal Medicine Teaching and Research, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yujia Chen
- Department of Internal Medicine Teaching and Research, The Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xin Zhou
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhuanfang Zheng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lingling Yang
- Department of Psychological Sleep, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yan Li
- Department of Psychological Sleep, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| |
Collapse
|
11
|
Hu W, Zhu QL, Zheng JL, Wen ZY. Cadmium induced oxidative stress, endoplasmic reticulum (ER) stress and apoptosis with compensative responses towards the up-regulation of ribosome, protein processing in the ER, and protein export pathways in the liver of zebrafish. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 242:106023. [PMID: 34798301 DOI: 10.1016/j.aquatox.2021.106023] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/09/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
The present study identified that exposure to 5, 10, and 20 µg/L Cd for 48 days reduced growth, increased Cd accumulation and levels of reactive oxygen species (ROS) and lipid peroxidation, and induced ER stress and cellular apoptosis in the liver in a dose-dependent manner. However, the survival rate was not affected by Cd. The increased production of ROS might result from reduced catalase (CAT) and copper/zinc-superoxide dismutase (Cu/Zn-SOD) activities, which might trigger ER stress pathways and subsequently induce apoptotic responses, ultimately leading to growth inhibition. Transcriptomic analyses indicated that the differentially expressed genes (DEGs) involved in metabolic pathways were significantly enriched and dysregulated by Cd, suggesting that metabolic disturbances may contribute to Cd toxicity. However, there were increases in glutathione peroxidase (GPX) activity, protein levels of metallothioneins (MTs) and heat shock protein 70 (HSP70), and mRNA levels of sod1, cat, gpx, mt2, and hsp70. Furthermore, DEGs related to ribosome, protein processing in the ER, and protein export pathways were significantly enriched and up-regulated by Cd. These increases may be compensatory responses following oxidative stress, ER stress, and apoptosis to resist negative effects. Taken together, we demonstrated that environmentally relevant levels of Cd induced adaptive responses with compensatory mechanisms in fish, which may help to maintain fish survival at the cost of growth.
Collapse
Affiliation(s)
- Wei Hu
- School of Animal Science, Yangtze University, Jingzhou, 424020, PR China
| | - Qing-Ling Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China.
| | - Jia-Lang Zheng
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China.
| | - Zheng-Yong Wen
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, China
| |
Collapse
|
12
|
Zheng JL, Peng LB, Xia LP, Li J, Zhu QL. Effects of continuous and intermittent cadmium exposure on HPGL axis, GH/IGF axis and circadian rhythm signaling and their consequences on reproduction in female zebrafish: Biomarkers independent of exposure regimes. CHEMOSPHERE 2021; 282:130879. [PMID: 34087554 DOI: 10.1016/j.chemosphere.2021.130879] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
Typical biomarkers of cadmium (Cd) pollution have well been confirmed in fish from continuous exposure pattern. However, in a natural environment, fish may be exposed to Cd intermittently. In this study, juvenile female zebrafish were exposed for 48 days to 10 μg/L Cd continuously, 20 μg/L for 1 day in every 2 days or 30 μg/L for 1 day in every 3 days. The toxic effects were evaluated using 8 various physiological and biochemical endpoints like specific growth rate (SGR), 17β-estradiol (E2) and vitellogenin (VTG) concentrations in plasma, reproductive parameters (gonadosomatic index (GSI), egg-laying amount, spawning percentage, and hatching and mortality rate of embryos). Transcription of 59 genes related to hypothalamic-pituitary-gonadal-liver (HPGL) axis, circadian rhythm signaling and insulin-like growth factor (IGF) system was examined. SGR, spawning percentage, E2 and VTG levels declined in fish exposed to 10 and 20 μg/L Cd but remained relatively stable in fish exposed to 30 μg/L Cd. Exposure to 10, 20 and 30 μg/L Cd significantly reduced GSI, hatching rate and mortality rate. Similarly, mRNA expression of 27 genes were sensitive to both continuous and intermittent Cd exposure. Among these genes, expression levels of 10 genes had more than 5-fold increase or decrease, including mRNA levels of vtg1, vtg2, vtg3, esr1, igf2a, igf2b, igfbp5b, nr1d1, gnrh3 and gnrhr4. The most sensitive molecular biomarker was vtg3 expression with 1500-3100 fold increase in the liver. The present study, for the first time, provides effective candidate biomarkers for Cd, which are independent of exposure regimes.
Collapse
Affiliation(s)
- Jia-Lang Zheng
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, PR China.
| | - Li-Bin Peng
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, PR China
| | - Li-Ping Xia
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, PR China
| | - Jiji Li
- College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China
| | - Qing-Ling Zhu
- College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, PR China.
| |
Collapse
|
13
|
Wu C, Wang D, Niu K, Feng Q, Chen H, Zhu H, Xiang H. Gene expression profiling in peripheral blood lymphocytes for major depression: preliminary cues from Chinese discordant sib-pair study. Transl Psychiatry 2021; 11:540. [PMID: 34667146 PMCID: PMC8526709 DOI: 10.1038/s41398-021-01665-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022] Open
Abstract
The etiology of major depressive disorder (MDD) involves many factors such as heredity and environment. There are very few MDD-related studies in Chinese population using twin or sib-pairs for depression-control samples. Here we used the microarray approach and compared gene expression profiling of peripheral blood lymphocytes from 6 sib-pairs discordant on lifetime history of MDD. Within sib-pair differentially expressed genes are obvious fewer in the 1st, 2nd, and 5th compared with those in the 3rd, 4th, and 6th sib-pairs. Gene expression pattern of these DEGs distinguished MDD individuals from the normal one in 3rd, 4th, and 6th sib-pair but not in the 1st, 2nd, and 5th pair, suggesting heterogeneity of different sib-pairs and somewhat commonalities among the 3rd, 4th, and 6th sib-pairs. Comprehensive protein interaction network analysis revealed two key genes PTH and FGF2 in a dominant network where the majority of the genes were significantly down-regulated. PTH was significantly down-regulated in all the sib-pairs while FGF2 was in the 3rd, 4th, and 6th sib-pairs. KEGG enrichment analysis of all the DEGs in networks showed that PTH and related genes were significantly enriched in the pathway of parathyroid hormone secretion, synthesis, and action while FGF2 and related genes were significantly enriched in the pathways of cancer and specifically breast cancer. Generally reduced expression of these genes in peripheral blood lymphocytes of MDD individuals implied their functional repression associated with MDD. Pending validation in more samples, the findings in this study provided valuable cues for understanding the potential mechanism of MDD, as well as potential markers for the diagnosis and treatment of depression in the Chinese population.
Collapse
Affiliation(s)
- Chan Wu
- grid.459864.20000 0004 6005 705XSouth China Normal University-Panyu Central Hospital Joint Laboratory of Basic and Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China ,grid.263785.d0000 0004 0368 7397Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Danfeng Wang
- grid.410737.60000 0000 8653 1072The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kangkang Niu
- grid.263785.d0000 0004 0368 7397Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Qili Feng
- grid.459864.20000 0004 6005 705XSouth China Normal University-Panyu Central Hospital Joint Laboratory of Basic and Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China ,grid.263785.d0000 0004 0368 7397Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Hanwei Chen
- grid.459864.20000 0004 6005 705XSouth China Normal University-Panyu Central Hospital Joint Laboratory of Basic and Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Haibing Zhu
- South China Normal University-Panyu Central Hospital Joint Laboratory of Basic and Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China. .,Department of Psychiatry, Guangzhou Panyu Central Hospital, Guangzhou, China.
| | - Hui Xiang
- South China Normal University-Panyu Central Hospital Joint Laboratory of Basic and Translational Medical Research, Guangzhou Panyu Central Hospital, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
14
|
Quantitative proteomic analysis of trachea in fatting pig exposed to ammonia. J Proteomics 2021; 247:104330. [PMID: 34302998 DOI: 10.1016/j.jprot.2021.104330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/06/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
Ammonia (NH3) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH3 is lacking, which is crucial to understanding how NH3 induces respiratory damage. In this study, we performed labeled quantitative proteomic (TMT-MS) analysis in the trachea of fatting pigs exposed to NH3 for 30 days. The proteomic results were then validated by Immunohistochemistry (IHC) and Parallel Reaction Monitoring (PRM). The results showed that a total of 126 differentially abundant proteins (DAPs) were identified (fold change <0.83 or > 1.2 and P < 0.05), including 70 differentially up-regulated proteins (DUPs) and 56 differentially down-regulated proteins (DDPs). These proteins were mainly located in intracellular regions and involved in immune response, metabolism and protein synthesis. The results of DAPs (EHHADH, RPL28, SLC25A6, TUBB6, CD14, CTSS, RPS11, RPL19, SLC25A5, RPS8, FABP3, RPL21, RPL34, RPL32, PDIA3, FBP1, HSPH1, SAR1A and SEC24C) verified by IHC and PRM were consistent with the proteomic results. The results of this study provided a basis and a novel insight for understanding the mechanism of NH3-induced tracheal injury. SIGNIFICANCE: Ammonia (NH3) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH3 is lacking, which is crucial to understanding how NH3 induces respiratory damage. Therefore, in this study, labeled quantitative proteomics (TMT-MS) was used to detect trachea tissue samples from finishing pigs in NH3 exposure group and control group, and PRM method was used to further verify the highly abundant proteins in NH3 exposure samples, so as to identify new diagnostic markers for NH3 poisoning. The results of this study provided a basis and a novel insight for understanding the molecular pathological mechanism of NH3-induced tracheal injury.
Collapse
|
15
|
Zuo Y, Wei D, Zhu C, Naveed O, Hong W, Yang X. Unveiling the Pathogenesis of Psychiatric Disorders Using Network Models. Genes (Basel) 2021; 12:1101. [PMID: 34356117 PMCID: PMC8304351 DOI: 10.3390/genes12071101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
Psychiatric disorders are complex brain disorders with a high degree of genetic heterogeneity, affecting millions of people worldwide. Despite advances in psychiatric genetics, the underlying pathogenic mechanisms of psychiatric disorders are still largely elusive, which impedes the development of novel rational therapies. There has been accumulating evidence suggesting that the genetics of complex disorders can be viewed through an omnigenic lens, which involves contextualizing genes in highly interconnected networks. Thus, applying network-based multi-omics integration methods could cast new light on the pathophysiology of psychiatric disorders. In this review, we first provide an overview of the recent advances in psychiatric genetics and highlight gaps in translating molecular associations into mechanistic insights. We then present an overview of network methodologies and review previous applications of network methods in the study of psychiatric disorders. Lastly, we describe the potential of such methodologies within a multi-tissue, multi-omics approach, and summarize the future directions in adopting diverse network approaches.
Collapse
Affiliation(s)
- Yanning Zuo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Don Wei
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Carissa Zhu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Ormina Naveed
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Weizhe Hong
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
16
|
Yang C, Kang L, Zhao Q. Comparative transcriptomic analysis of the l-4i silkworm (Lepidoptera: Bombyx mori) mutants and its wild-type strain P33 by RNA-Seq. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100800. [PMID: 33607576 DOI: 10.1016/j.cbd.2021.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 10/22/2022]
Abstract
The silkworm (Bombyx mori) is a domesticated holometabolous insect, and more than 400 Mendelian mutations have been identified. Investigating the mechanism behind these silkworm mutants is essential for understanding the development of silkworms and other lepidopterans, and lethal genes could be used for pest control. The lethal silkworm mutant in the fourth instar (l-4i) has been recently found; however, the underlying mechanism is not yet clear. Herein, we studied the l-4i mutant and its wild-type strain P33 using RNA sequencing (RNA-seq). Our results revealed that 2013 genes were significantly downregulated, and 20 biological processes, including spliceosomal snRNP assembly, protein folding and protein catabolic process, were significantly enriched in these downregulated genes. Moreover, 2405 genes were significantly upregulated in the l-4i mutant, and 20 biological processes, including purine nucleobase metabolic process, nucleoside metabolic process and de novo IMP biosynthetic process, were significantly enriched in these upregulated genes. The study suggests that the imbalance of multiple biological processes and pathways and abnormal protein generation from RNA alternative splicing may cause the death of the l-4i mutant.
Collapse
Affiliation(s)
- Chenjie Yang
- School of Biotechnology, Jiangsu University of Science and Technology, Nanxv Road, Zhenjiang, Jiangsu 212018, China; The Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Lequn Kang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Qiaoling Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Nanxv Road, Zhenjiang, Jiangsu 212018, China; The Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China.
| |
Collapse
|
17
|
Soares E, Reis J, Rodrigues M, Ribeiro CF, Pereira FC. Circulating Extracellular Vesicles: The Missing Link between Physical Exercise and Depression Management? Int J Mol Sci 2021; 22:ijms22020542. [PMID: 33430399 PMCID: PMC7827999 DOI: 10.3390/ijms22020542] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022] Open
Abstract
Depression is associated with an increased risk of aging-related diseases. It is also seemingly a common psychological reaction to pandemic outbreaks with forced quarantines and lockdowns. Thus, depression represents, now more than ever, a major global health burden with therapeutic management challenges. Clinical data highlights that physical exercise is gaining momentum as a non-pharmacological intervention in depressive disorders. Although it may contribute to the reduction of systemic inflammation associated with depression, the mechanisms underlying the beneficial physical exercise effects in emotional behavior remain to be elucidated. Current investigations indicate that a rapid release of extracellular vesicles into the circulation might be the signaling mediators of systemic adaptations to physical exercise. These biological entities are now well-established intercellular communicators, playing a major role in relevant physiological and pathophysiological functions, including brain cell-cell communication. We also reviewed emerging evidence correlating depression with modified circulating extracellular vesicle surfaces and cargo signatures (e.g., microRNAs and proteins), envisioned as potential biomarkers for diagnosis, efficient disease stratification and appropriate therapeutic management. Accordingly, the clinical data summarized in the present review prompted us to hypothesize that physical exercise-related circulating extracellular vesicles contribute to its antidepressant effects, particularly through the modulation of inflammation. This review sheds light on the triad "physical exercise-extracellular vesicles-depression" and suggests new avenues in this novel emerging field.
Collapse
Affiliation(s)
- Edna Soares
- Institute of Pharmacology and Experimental Therapeutics/IBILI, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (J.R.); (M.R.); (C.F.R.)
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-504 Coimbra, Portugal
- Correspondence: (E.S.); (F.C.P.)
| | - Julie Reis
- Institute of Pharmacology and Experimental Therapeutics/IBILI, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (J.R.); (M.R.); (C.F.R.)
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-504 Coimbra, Portugal
| | - Mariana Rodrigues
- Institute of Pharmacology and Experimental Therapeutics/IBILI, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (J.R.); (M.R.); (C.F.R.)
| | - Carlos Fontes Ribeiro
- Institute of Pharmacology and Experimental Therapeutics/IBILI, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (J.R.); (M.R.); (C.F.R.)
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-504 Coimbra, Portugal
| | - Frederico C. Pereira
- Institute of Pharmacology and Experimental Therapeutics/IBILI, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (J.R.); (M.R.); (C.F.R.)
- Faculty of Medicine, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-504 Coimbra, Portugal
- Correspondence: (E.S.); (F.C.P.)
| |
Collapse
|
18
|
Zeng D, He S, Ma C, Wen Y, Song W, Xu Q, Zhao N, Wang Q, Yu Y, Shen Y, Huang J, Li H. Network-based approach to identify molecular signatures in the brains of depressed suicides. Psychiatry Res 2020; 294:113513. [PMID: 33137553 DOI: 10.1016/j.psychres.2020.113513] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Suicide is a serious and global health problem that has a strong association with major depressive disorder (MDD). Weighted gene co-expression network analysis (WGCNA) was performed for the construction of a co-expression network to get important gene modules associated with depressed suicide. METHODS Transcriptome sequencing data from dorsolateral prefrontal cortex was used, which included 29 non-psychiatric controls (CON), 21 MDD suicides (MDD-S) and 9 MDD non-suicides (MDD-NS) of medication-free sudden death individuals. RESULTS The highest correlation in the module-traits relationship was discovered between the black module and suicide (r = -0.30, p = 0.024) as well as MDD (r = -0.34, p = 0.010).Furthermore, the expression levels of genes decreased progressively across the three groups (CON>MDD-NS>MDD-S). Therefore, the genes in the black module was selected for subsequent analyses. Protein-Protein Interaction Network found that the top 10 hub genes were somehow involved in depressed suicide including JUN, FOS, ATF3, MYC, EGR1, FOSB, DUSP1, NFKBIA, TLR2, NR4A1. Most of the GO terms were enriched in cell death and apoptosis and KEGG was mainly enriched in MAPK pathway. Cell Type-Specific Analysis found these genes were significantly enriched in endothelial and microglia (p<0.000) cell types. In addition, 92 genes in this module had at least one highly significant differentially methylated positions between MDD-S and controls. CONCLUSION Cell death and apoptosis may participate in the interplay between depressed suicide and neuro-inflammation system.
Collapse
Affiliation(s)
- Duan Zeng
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Shen He
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Changlin Ma
- Shanghai Jiading District Mental Health Center, Shanghai, PR China
| | - Yi Wen
- Shanghai Jiading District Mental Health Center, Shanghai, PR China
| | - Weichen Song
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.
| | - Qingqing Xu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Nan Zhao
- Department of Psychiatry, Shanghai Pudong New Area Mental Health Center, Tongji University School of Medicine, Shanghai, PR China
| | - Qiang Wang
- Department of Psychiatry, Shanghai Pudong New Area Mental Health Center, Tongji University School of Medicine, Shanghai, PR China
| | - Yimin Yu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Clinical Research Center for Mental Health, Shanghai, PR China
| | - Yifeng Shen
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Clinical Research Center for Mental Health, Shanghai, PR China
| | - Jingjing Huang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Clinical Research Center for Mental Health, Shanghai, PR China.
| | - Huafang Li
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Clinical Research Center for Mental Health, Shanghai, PR China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, PR China.
| |
Collapse
|
19
|
Guo D, Zhang S, Tang Z, Wang H. Construction of gene-classifier and co-expression network analysis of genes in association with major depressive disorder. Psychiatry Res 2020; 293:113387. [PMID: 32823199 DOI: 10.1016/j.psychres.2020.113387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/10/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Because the pathogenesis of major depressive disorder (MDD) is still unclear and the accurate diagnosis remains unavailable, we aimed to analyze its molecular mechanisms and develop a gene classifier to improve diagnostic accuracy. We extracted differentially expressed genes from two datasets, GSE45642 (from brain tissue samples) and GSE98793 (from blood samples), and found three key modules to have a significant correlation with MDD traits by weighted gene coexpression network analysis. Hub genes were identified from the key modules according to the connectivity degree in the network and subjected to least absolute shrinkage and selection operator regression analysis. A total of eighty-five hub genes were selected to construct the gene classifier, which had considerable ability to recognize MDD patients in the training set and test set. In addition, the relationship between the key MDD modules and brain tissues indicated that the anterior cingulate should be a notable region in the study of MDD pathogenesis. The results of Gene Ontology (GO) and pathway enrichment analyses reiterate the relationship between depression and immunity. Therefore we identified MDD hub genes in the InnateDB database, and found 14 genes involved in both MDD and the inflammatory response.
Collapse
Affiliation(s)
- Dongmei Guo
- Department of Biochemistry, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shumin Zhang
- Department of Biochemistry, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Zhen Tang
- Department of Biochemistry, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Hanyan Wang
- Department of Biochemistry, North Sichuan Medical College, Nanchong, Sichuan, China.
| |
Collapse
|
20
|
Wong MWK, Thalamuthu A, Braidy N, Mather KA, Liu Y, Ciobanu L, Baune BT, Armstrong NJ, Kwok J, Schofield P, Wright MJ, Ames D, Pickford R, Lee T, Poljak A, Sachdev PS. Genetic and environmental determinants of variation in the plasma lipidome of older Australian twins. eLife 2020; 9:e58954. [PMID: 32697195 PMCID: PMC7394543 DOI: 10.7554/elife.58954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
The critical role of blood lipids in a broad range of health and disease states is well recognised but less explored is the interplay of genetics and environment within the broader blood lipidome. We examined heritability of the plasma lipidome among healthy older-aged twins (75 monozygotic/55 dizygotic pairs) enrolled in the Older Australian Twins Study (OATS) and explored corresponding gene expression and DNA methylation associations. 27/209 lipids (13.3%) detected by liquid chromatography-coupled mass spectrometry (LC-MS) were significantly heritable under the classical ACE twin model (h2 = 0.28-0.59), which included ceramides (Cer) and triglycerides (TG). Relative to non-significantly heritable TGs, heritable TGs had a greater number of associations with gene transcripts, not directly associated with lipid metabolism, but with immune function, signalling and transcriptional regulation. Genome-wide average DNA methylation (GWAM) levels accounted for variability in some non-heritable lipids. We reveal a complex interplay of genetic and environmental influences on the ageing plasma lipidome.
Collapse
Affiliation(s)
- Matthew WK Wong
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- Neuroscience Research AustraliaSydneyAustralia
| | - Yue Liu
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Liliana Ciobanu
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- The University of Adelaide, Adelaide Medical School, Discipline of PsychiatryAdelaideAustralia
| | - Bernhardt T Baune
- The University of Adelaide, Adelaide Medical School, Discipline of PsychiatryAdelaideAustralia
- Department of Psychiatry, University of MünsterMünsterGermany
- Department of Psychiatry, Melbourne Medical School, The University of MelbourneMelbourneAustralia
- The Florey Institute of Neuroscience and Mental Health, The University of MelbourneMelbourneAustralia
| | | | - John Kwok
- Brain and Mind Centre, The University of SydneySydneyAustralia
| | - Peter Schofield
- Neuroscience Research AustraliaSydneyAustralia
- School of Medical Sciences, University of New South WalesSydneyAustralia
| | - Margaret J Wright
- Queensland Brain Institute, University of QueenslandBrisbaneAustralia
- Centre for Advanced Imaging, University of QueenslandBrisbaneAustralia
| | - David Ames
- University of Melbourne Academic Unit for Psychiatry of Old AgeKewAustralia
- National Ageing Research InstituteParkvilleAustralia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South WalesSydneyAustralia
| | - Teresa Lee
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales HospitalSydneyAustralia
| | - Anne Poljak
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- School of Medical Sciences, University of New South WalesSydneyAustralia
- Bioanalytical Mass Spectrometry Facility, University of New South WalesSydneyAustralia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales HospitalSydneyAustralia
| |
Collapse
|
21
|
Ciobanu LG, Sachdev PS, Trollor JN, Reppermund S, Thalamuthu A, Mather KA, Cohen-Woods S, Stacey D, Toben C, Schubert KO, Baune BT. Downregulated transferrin receptor in the blood predicts recurrent MDD in the elderly cohort: A fuzzy forests approach. J Affect Disord 2020; 267:42-48. [PMID: 32063571 DOI: 10.1016/j.jad.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND At present, no predictive markers for Major Depressive Disorder (MDD) exist. The search for such markers has been challenging due to clinical and molecular heterogeneity of MDD, the lack of statistical power in studies and suboptimal statistical tools applied to multidimensional data. Machine learning is a powerful approach to mitigate some of these limitations. METHODS We aimed to identify the predictive markers of recurrent MDD in the elderly using peripheral whole blood from the Sydney Memory and Aging Study (SMAS) (N = 521, aged over 65) and adopting machine learning methodology on transcriptome data. Fuzzy Forests is a Random Forests-based classification algorithm that takes advantage of the co-expression network structure between genes; it allows to alleviate the problem of p >> n via reducing the dimensionality of transcriptomic feature space. RESULTS By adopting Fuzzy Forests on transcriptome data, we found that the downregulated TFRC (transferrin receptor) can predict recurrent MDD with an accuracy of 63%. LIMITATIONS Although we corrected our data for several important confounders, we were not able to account for the comorbidities and medication taken, which may be numerous in the elderly and might have affected the levels of gene transcription. CONCLUSIONS We found that downregulated TFRC is predictive of recurrent MDD, which is consistent with the previous literature, indicating the role of the innate immune system in depression. This study is the first to successfully apply Fuzzy Forests methodology on psychiatric condition, opening, therefore, a methodological avenue that can lead to clinically useful predictive markers of complex traits.
Collapse
Affiliation(s)
- Liliana G Ciobanu
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, South Australia, Australia; Quality Use of Medicines and Pharmacy Research Centre, School of Pharmacy and Medical Sciences, University of South Australia, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, UNSW Sydney, New South Wales, Australia
| | - Julian N Trollor
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, UNSW Sydney, New South Wales, Australia; Department of Developmental Disability Neuropsychiatry, School of Psychiatry, UNSW Sydney, New South Wales, Australia
| | - Simone Reppermund
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, UNSW Sydney, New South Wales, Australia; Department of Developmental Disability Neuropsychiatry, School of Psychiatry, UNSW Sydney, New South Wales, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, UNSW Sydney, New South Wales, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing (CHeBA), School of Psychiatry, UNSW Sydney, New South Wales, Australia; Neuroscience Research Australia, Randwick, Australia
| | - Sarah Cohen-Woods
- School of Psychology, Flinders University, South Australia, Australia
| | - David Stacey
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Catherine Toben
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, South Australia, Australia
| | - K Oliver Schubert
- Discipline of Psychiatry, Adelaide Medical School, The University of Adelaide, South Australia, Australia; Northern Adelaide Local Health Network, Mental Health Services, Lyell McEwin Hospital, Elizabeth Vale, South Australia, Australia
| | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany; Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
22
|
Comparison of serum microbiome composition in bipolar and major depressive disorders. J Psychiatr Res 2020; 123:31-38. [PMID: 32028208 DOI: 10.1016/j.jpsychires.2020.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/20/2022]
Abstract
Bipolar disorder and major depressive disorder are debilitating psychiatric conditions which can be difficult to differentiate; however, recent studies have suggested that microbiome composition may be a potential tool in distinguishing between these two disorders. This study aimed to compare the serum microbiome composition of patients with bipolar disorder, major depressive disorder, and healthy controls. Serum samples were collected from 42 subjects with bipolar disorder, 30 with major depressive disorder, and 36 healthy controls. Bacterial DNA was isolated from bacteria-derived extracellular vesicles in the serum and then amplified and quantified with primers specific to the V3-V4 hypervariable region of the 16S rDNA gene. Sequence reads were clustered into operational taxonomic units and classified using the SILVA database. Alpha and beta diversity, individual taxa analysis based on phylum and genus, and functional pathways were compared. There was no statistical difference between alpha or beta diversity in patients with bipolar disorder and major depressive disorder; however, the Prevotella 2 and Ruminococcaceae UCG-002 genera were significantly more prevalent in patients with major depressive disorder than in either those with bipolar disorder or in healthy controls. Functional analysis of pathways revealed that the apoptosis function differed between all three groups. In conclusion, the Prevotella 2 and Ruminococcaceae UCG-002 genera were identified as potential candidates for distinguishing bipolar disorder and major depressive disorder. Further studies with larger sample sizes, longitudinal designs, and control for other various confounders are warranted.
Collapse
|
23
|
Liu W, Zhang L, Zheng D, Zhang Y. Umbilical cord blood-based gene signatures related to prenatal major depressive disorder. Medicine (Baltimore) 2019; 98:e16373. [PMID: 31305436 PMCID: PMC6641773 DOI: 10.1097/md.0000000000016373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Prenatal exposure to depression has been considered as a risk factor for adverse childhood, while it is accompanied by unknown molecular mechanisms. The aim of this study was to identify differentially expressed genes (DEGs) and associated biological processes between cord blood samples from neonates born to mothers who exposed to major depressive disorder (MDD) and healthy mothers. METHODS The microarray data GSE114852 were downloaded to analyze the mRNA expression profiles of umbilical cord blood with 31 samples exposed to prenatal MDD and 62 samples with healthy mothers. Kyoto Encyclopedia of Genes and Genomes pathway and Gene ontology enrichment analyses were conducted to identify associated biochemical pathways and functional categories of the DEGs. The protein-protein interaction network was constructed and the top 10 hub genes in the network were predicted. RESULTS The results showed several immunity related processes, such as "phagosome", "Epstein-Barr virus infection", "proteasome", "positive regulation of I-kappaB kinase/NF-kappaB signaling", "interferon-gamma-mediated signaling pathway", and "tumor necrosis factor" presented significant differences between two groups. Most of the hub genes (for example PSMD2, PSMD6, PSMB8, PSMB9) were also associated with immune pathways. CONCLUSION This bioinformatic analysis demonstrated immune-mediated mechanisms might play a fatal role in abnormalities in fetal gene expression profiles caused by prenatal MDD.
Collapse
Affiliation(s)
- Wenhua Liu
- Department of Psychology and Mental Health, Huaihe Hospital of Henan University, Kaifeng City, Henan Province
| | - Lan Zhang
- Department of Psychology and Mental Health, Second Affiliated Hospital of Lanzhou University, Lanzhou City, Gansu Province
| | | | - Yijie Zhang
- Department of Respiratory and Critical Care Medicine, Huaihe Hospital of Henan University, Kaifeng City, Henan Province, China
| |
Collapse
|
24
|
Clark SR, Schubert KO, Olagunju AT, Lyrtzis EA, Baune BT. Cognitive and Functional Assessment of Psychosis Stratification Study (CoFAPSS): Rationale, Design, and Characteristics. Front Psychiatry 2018; 9:662. [PMID: 30559688 PMCID: PMC6287598 DOI: 10.3389/fpsyt.2018.00662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
Prediction of treatment response and illness trajectory in psychotic disorders including schizophrenia, bipolar affective disorder, schizoaffective disorder, and psychotic depression is difficult due to heterogeneity in presentation and outcome. Consequently, patients may receive prolonged ineffective treatments leading to functional decline, illness chronicity, and iatrogenic physical illness. One approach to addressing these problems is to stratify patients based on historical, clinical, and biological signatures. Such an approach has the potential to improve categorization resulting in better understanding of underlying mechanisms and earlier evidence-based treatment with reduced side effect burden. To investigate these multimodal signatures we developed the Cognitive and Functional Assessment of Psychosis Stratification Study (CoFAPSS) employing a prospective study design and a healthy control group comparison. The main aim of this study is to investigate cognitive, and biological "genomics" markers of psychotic illnesses that can be integrated with clinical data to improve prediction of risk and define functional trajectories. We also aim to identify biological "genomic" signatures underpinning variation in treatment response and adverse medical outcomes. The study commenced in June 2016, including patients with primary diagnosis of psychotic disorders including schizophrenia, bipolar affective disorder, schizoaffective disorder, and psychotic depression according to DSM-5 criteria. The assessment covers a wide range of participant history (life stressors, trauma, and family history), cognitive dimensions (social perception, memory and learning, attention, executive function, and general cognition), measures to assess psychosocial function and quality of life, psychotic symptom severity, clinical course of illness, and parameters for adverse medical outcome. Blood is collected for comprehensive genomic discovery analyses of biological (genomic, transcriptomic, proteomic, and cell-biologic) markers. The CoFAPSS is a novel approach that integrates clinical, cognitive and biological "genomic" markers to clarify clinico-pathological basis of risk, functional trajectories, disease stratification, treatment response, and adverse medical outcome. The CoFAPSS team welcomes collaborations with both national and international investigators.
Collapse
Affiliation(s)
- Scott R Clark
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia
| | - K Oliver Schubert
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia
| | - Andrew T Olagunju
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia.,Department of Psychiatry University of Lagos, Lagos, Nigeria
| | - Ellen Alexandra Lyrtzis
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia
| | - Bernhard T Baune
- Discipline of Psychiatry, School of Medicine, The University of Adelaide Adelaide, SA, Australia.,Department of Psychiatry, Melbourne Medical School, The University of Melbourne Melbourne, VIC, Australia
| |
Collapse
|