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Xu S, Williams J, Ferreira MAR. BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data. BMC Bioinformatics 2023; 24:343. [PMID: 37715138 PMCID: PMC10503129 DOI: 10.1186/s12859-023-05468-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: 01/30/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWASes) aim to identify single nucleotide polymorphisms (SNPs) associated with a given phenotype. A common approach for the analysis of GWAS is single marker analysis (SMA) based on linear mixed models (LMMs). However, LMM-based SMA usually yields a large number of false discoveries and cannot be directly applied to non-Gaussian phenotypes such as count data. RESULTS We present a novel Bayesian method to find SNPs associated with non-Gaussian phenotypes. To that end, we use generalized linear mixed models (GLMMs) and, thus, call our method Bayesian GLMMs for GWAS (BG2). To deal with the high dimensionality of GWAS analysis, we propose novel nonlocal priors specifically tailored for GLMMs. In addition, we develop related fast approximate Bayesian computations. BG2 uses a two-step procedure: first, BG2 screens for candidate SNPs; second, BG2 performs model selection that considers all screened candidate SNPs as possible regressors. A simulation study shows favorable performance of BG2 when compared to GLMM-based SMA. We illustrate the usefulness and flexibility of BG2 with three case studies on cocaine dependence (binary data), alcohol consumption (count data), and number of root-like structures in a model plant (count data).
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Affiliation(s)
- Shuangshuang Xu
- Department of Statistics, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jacob Williams
- Department of Statistics, Virginia Tech, Blacksburg, VA, 24061, USA
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Li J, Wu Y, Xue T, He J, Zhang L, Liu Y, Zhao J, Chen Z, Xie M, Xiao B, Ye Y, Qin S, Tang Q, Huang M, Zhu H, Liu N, Guo F, Zhang L, Zhang L. Cdc42 signaling regulated by dopamine D2 receptor correlatively links specific brain regions of hippocampus to cocaine addiction. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166569. [PMID: 36243293 DOI: 10.1016/j.bbadis.2022.166569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/18/2022] [Accepted: 10/06/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Hippocampus plays critical roles in drug addiction. Cocaine-induced modifications in dopamine receptor function and the downstream signaling are important regulation mechanisms in cocaine addiction. Rac regulates actin filament accumulation while Cdc42 stimulates the formation of filopodia and neurite outgrowth. Based on the region specific roles of small GTPases in brain, we focused on the hippocampal subregions to detect the regulation of Cdc42 signaling in long-term morphological and behavioral adaptations to cocaine. METHODS Genetically modified mouse models of Cdc42, dopamine receptor D1 (D1R) and D2 (D2R) and expressed Cdc42 point mutants that are defective in binding to and activation of its downstream effector molecules PAK and N-WASP were generated, respectively, in CA1 or dentate gyrus (DG) subregion. RESULTS Cocaine induced upregulation of Cdc42 signaling activity. Cdc42 knockout or mutants blocked cocaine-induced increase in spine plasticity in hippocampal CA1 pyramidal neurons, leading to a decreased conditional place preference (CPP)-associated memories and spatial learning and memory in water maze. Cdc42 knockout or mutants promoted cocaine-induced loss of neurogenesis in DG, leading to a decreased CPP-associated memories and spatial learning and memory in water maze. Furthermore, by using D1R knockout, D2R knockout, and D2R/Cdc42 double knockout mice, we found that D2R, but not D1R, regulated Cdc42 signaling in cocaine-induced neural plasticity and behavioral changes. CONCLUSIONS Cdc42 acts downstream of D2R in the hippocampus and plays an important role in cocaine-induced neural plasticity through N-WASP and PAK-LIMK-Cofilin, and Cdc42 signaling pathway correlatively links specific brain regions (CA1, dentate gyrus) to cocaine-induced CPP behavior.
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Affiliation(s)
- Juan Li
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Histology and Embryology, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Key Laboratory of Construction and Detection in Tissue Engineering of Guangdong Province, School of Basic Medical Sciences, Center for Orthopaedic Surgery of the Third Affiliated Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yue Wu
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Tao Xue
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jing He
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Lei Zhang
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yutong Liu
- Department of Histology and Embryology, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Key Laboratory of Construction and Detection in Tissue Engineering of Guangdong Province, School of Basic Medical Sciences, Center for Orthopaedic Surgery of the Third Affiliated Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jinlan Zhao
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhenzhong Chen
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Minjuan Xie
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Bin Xiao
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yingshan Ye
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Sifei Qin
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qingqiu Tang
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Mengfan Huang
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hangfei Zhu
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - N Liu
- Institute of Comparative Medicine & Laboratory Animal Center, Elderly Health Services Research Center, Southern Medical University, Guangzhou 510515, China
| | - Fukun Guo
- Division of Experimental Hematology and Cancer Biology, Children's Hospital Research Foundation, Cincinnati, OH, USA
| | - Lin Zhang
- Department of Histology and Embryology, NMPA Key Laboratory for Safety Evaluation of Cosmetics, Key Laboratory of Construction and Detection in Tissue Engineering of Guangdong Province, School of Basic Medical Sciences, Center for Orthopaedic Surgery of the Third Affiliated Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Lu Zhang
- Guangdong Provincial Key Laboratory of Functional Proteomics, Key Laboratory of Mental Health of the Ministry of Education, School of Basic Medical Sciences, Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China.
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Ronaldson PT, Davis TP. Transport Mechanisms at the Blood-Brain Barrier and in Cellular Compartments of the Neurovascular Unit: Focus on CNS Delivery of Small Molecule Drugs. Pharmaceutics 2022; 14:1501. [PMID: 35890396 PMCID: PMC9324459 DOI: 10.3390/pharmaceutics14071501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
Ischemic stroke is a primary origin of morbidity and mortality in the United States and around the world. Indeed, several research projects have attempted to discover new drugs or repurpose existing therapeutics to advance stroke pharmacotherapy. Many of these preclinical stroke studies have reported positive results for neuroprotective agents; however, only one compound (3K3A-activated protein C (3K3A-APC)) has advanced to Phase III clinical trial evaluation. One reason for these many failures is the lack of consideration of transport mechanisms at the blood-brain barrier (BBB) and neurovascular unit (NVU). These endogenous transport processes function as a "gateway" that is a primary determinant of efficacious brain concentrations for centrally acting drugs. Despite the knowledge that some neuroprotective agents (i.e., statins and memantine) are substrates for these endogenous BBB transporters, preclinical stroke studies have largely ignored the role of transporters in CNS drug disposition. Here, we review the current knowledge on specific BBB transporters that either limit drug uptake into the brain (i.e., ATP-binding cassette (ABC) transporters) or can be targeted for optimized drug delivery (i.e., solute carrier (SLC) transporters). Additionally, we highlight the current knowledge on transporter expression in astrocytes, microglia, pericytes, and neurons with an emphasis on transport mechanisms in these cell types that can influence drug distribution within the brain.
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Affiliation(s)
- Patrick T. Ronaldson
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ 85724-5050, USA;
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