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Xu J, Casanave R, Chitre AS, Wang Q, Nguyen KM, Blake C, Wagle M, Cheng R, Polesskaya O, Palmer AA, Guo S. Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556529. [PMID: 37732200 PMCID: PMC10508786 DOI: 10.1101/2023.09.06.556529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Behavioral diversity is critical for population fitness. Individual differences in risk-taking are observed across species, but underlying genetic mechanisms and conservation are largely unknown. We examined dark avoidance in larval zebrafish, a motivated behavior reflecting an approach-avoidance conflict. Brain-wide calcium imaging revealed significant neural activity differences between approach-inclined versus avoidance-inclined individuals. We used a population of ∼6,000 to perform the first genome-wide association study (GWAS) in zebrafish, which identified 34 genomic regions harboring many genes that are involved in synaptic transmission and human psychiatric diseases. We used CRISPR to study several causal genes: serotonin receptor-1b ( htr1b ), nitric oxide synthase-1 ( nos1 ), and stress-induced phosphoprotein-1 ( stip1 ). We further identified 52 conserved elements containing 66 GWAS significant variants. One encoded an exonic regulatory element that influenced tissue-specific nos1 expression. Together, these findings reveal new genetic loci and establish a powerful, scalable animal system to probe mechanisms underlying motivation, a critical dimension of psychiatric diseases.
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Nguyen MH, Zhang W, Pankratz N, Lane J, Chitiboina P, Faucz FR, Mills JL, Stratakis CA, Tatsi C. Exploratory Study of the Association of Genetic Factors With Recovery of Adrenal Function in Cushing Disease. J Endocr Soc 2023; 7:bvad046. [PMID: 37153111 PMCID: PMC10161137 DOI: 10.1210/jendso/bvad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Indexed: 05/09/2023] Open
Abstract
Successful treatment of endogenous Cushing disease (CD) is often followed by a period of adrenal insufficiency (AI). We performed an exploratory study on genetic factors potentially involved in the hypothalamic-pituitary-adrenal (HPA) axis recovery in patients with CD after remission. We identified 90 patients who achieved remission after surgery and had a minimum of 3 months follow-up. Variants in a selected panel of genes that were rare in the general population and predicted as damaging in silico were retrieved from whole exome sequencing analysis. We did not identify any variant with significant correlation with recovery time after adjusting for multiple comparisons. On gene-specific analysis the BAG1 gene showed a correlation with shorter duration of postsurgical AI, but both patients with BAG1 variants later experienced a recurrence. After excluding patients with recurrence, no statistical association was recorded. To conclude, we did not identify a strong genetic modifier of HPA recovery in this exploratory study.
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Affiliation(s)
- Matthew H Nguyen
- Unit on Hypothalamic and Pituitary Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Zhang
- Academy of Mathematics and System Sciences, Chinese Academy of Sciences, Beijing 100045, China
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55454, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55454, USA
| | - Prashant Chitiboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fabio R Faucz
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - James L Mills
- Epidemiology Branch, Eunice Kennedy Shriver National Institutes of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Constantine A Stratakis
- Unit on Hypothalamic and Pituitary Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Christina Tatsi
- Correspondence: Christina Tatsi, MD, MHSc, PhD, Eunice Kennedy Shriver National Institutes of Child Health and Human Development (NICHD), NIH, 10 Center Drive, Building 10, NIH-Clinical Research Center, Room 1-3330, MSC1103, Bethesda, MD 20892, USA.
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Zhang L, Ju T, Jin X, Ji J, Han J, Zhou X, Yuan Z. Network regression analysis for binary and ordinal categorical phenotypes in transcriptome-wide association studies. Genetics 2022; 222:iyac153. [PMID: 36227056 PMCID: PMC9713396 DOI: 10.1093/genetics/iyac153] [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: 07/14/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022] Open
Abstract
Transcriptome-wide association studies aim to integrate genome-wide association studies and expression quantitative trait loci mapping studies for exploring the gene regulatory mechanisms underlying diseases. Existing transcriptome-wide association study methods primarily focus on 1 gene at a time. However, complex diseases are seldom resulted from the abnormality of a single gene, but from the biological network involving multiple genes. In addition, binary or ordinal categorical phenotypes are commonly encountered in biomedicine. We develop a proportional odds logistic model for network regression in transcriptome-wide association study, Proportional Odds LOgistic model for NEtwork regression in Transcriptome-wide association study, to detect the association between a network and binary or ordinal categorical phenotype. Proportional Odds LOgistic model for NEtwork regression in Transcriptome-wide association study relies on 2-stage transcriptome-wide association study framework. It first adopts the distribution-robust nonparametric Dirichlet process regression model in expression quantitative trait loci study to obtain the SNP effect estimate on each gene within the network. Then, Proportional Odds LOgistic model for NEtwork regression in Transcriptome-wide association study uses pointwise mutual information to represent the general relationship among the network nodes of predicted gene expression in genome-wide association study, followed by the association analysis with all nodes and edges involved in proportional odds logistic model. A key feature of Proportional Odds LOgistic model for NEtwork regression in Transcriptome-wide association study is its ability to simultaneously identify the disease-related network nodes or edges. With extensive realistic simulations including those under various between-node correlation patterns, we show Proportional Odds LOgistic model for NEtwork regression in Transcriptome-wide association study can provide calibrated type I error control and yield higher power than other existing methods. We finally apply Proportional Odds LOgistic model for NEtwork regression in Transcriptome-wide association study to analyze bipolar and major depression status and blood pressure from UK Biobank to illustrate its benefits in real data analysis.
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Affiliation(s)
- Liye Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Institute for Medical Dataology, Shandong University, Jinan, Shandong 250003, China
| | - Tao Ju
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Institute for Medical Dataology, Shandong University, Jinan, Shandong 250003, China
| | - Xiuyuan Jin
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Institute for Medical Dataology, Shandong University, Jinan, Shandong 250003, China
| | - Jiadong Ji
- Institute for Financial Studies, Shandong University, Jinan, Shandong 250100, China
| | - Jiayi Han
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Institute for Medical Dataology, Shandong University, Jinan, Shandong 250003, China
| | - Xiang Zhou
- Department of Biostatistics, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- Institute for Medical Dataology, Shandong University, Jinan, Shandong 250003, China
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Johnson JL. Mutations in Hsp90 Cochaperones Result in a Wide Variety of Human Disorders. Front Mol Biosci 2021; 8:787260. [PMID: 34957217 PMCID: PMC8694271 DOI: 10.3389/fmolb.2021.787260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/08/2021] [Indexed: 12/19/2022] Open
Abstract
The Hsp90 molecular chaperone, along with a set of approximately 50 cochaperones, mediates the folding and activation of hundreds of cellular proteins in an ATP-dependent cycle. Cochaperones differ in how they interact with Hsp90 and their ability to modulate ATPase activity of Hsp90. Cochaperones often compete for the same binding site on Hsp90, and changes in levels of cochaperone expression that occur during neurodegeneration, cancer, or aging may result in altered Hsp90-cochaperone complexes and client activity. This review summarizes information about loss-of-function mutations of individual cochaperones and discusses the overall association of cochaperone alterations with a broad range of diseases. Cochaperone mutations result in ciliary or muscle defects, neurological development or degeneration disorders, and other disorders. In many cases, diseases were linked to defects in established cochaperone-client interactions. A better understanding of the functional consequences of defective cochaperones will provide new insights into their functions and may lead to specialized approaches to modulate Hsp90 functions and treat some of these human disorders.
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Affiliation(s)
- Jill L Johnson
- Department of Biological Sciences and Center for Reproductive Biology, University of Idaho, Moscow, ID, United States
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