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Anderson JQ, Darakjian P, Hitzemann R, Lockwood DR, Phillips TJ, Ozburn AR. Brain gene expression differences related to ethanol preference in the collaborative cross founder strains. Front Behav Neurosci 2022; 16:992727. [PMID: 36212197 PMCID: PMC9539754 DOI: 10.3389/fnbeh.2022.992727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
The collaborative cross (CC) founder strains include five classical inbred laboratory strains [129S1/SvlmJ (S129), A/J (AJ), C57BL/6J (B6), NOD/ShiLtJ (NOD), and NZO/HILtJ (NZO)] and three wild-derived strains [CAST/EiJ (CAST), PWK/PhJ (PWK), and WSB/EiJ (WSB)]. These strains encompass 89% of the genetic diversity available in Mus musculus and ∼10-20 times more genetic diversity than found in Homo sapiens. For more than 60 years the B6 strain has been widely used as a genetic model for high ethanol preference and consumption. However, another of the CC founder strains, PWK, has been identified as a high ethanol preference/high consumption strain. The current study determined how the transcriptomes of the B6 and PWK strains differed from the 6 low preference CC strains across 3 nodes of the brain addiction circuit. RNA-Seq data were collected from the central nucleus of the amygdala (CeA), the nucleus accumbens core (NAcc) and the prelimbic cortex (PrL). Differential expression (DE) analysis was performed in each of these brain regions for all 28 possible pairwise comparisons of the CC founder strains. Unique genes for each strain were identified by selecting for genes that differed significantly [false discovery rate (FDR) < 0.05] from all other strains in the same direction. B6 was identified as the most distinct classical inbred laboratory strain, having the highest number of total differently expressed genes (DEGs) and DEGs with high log fold change, and unique genes compared to other CC strains. Less than 50 unique DEGs were identified in common between B6 and PWK within all three brain regions, indicating the strains potentially represent two distinct genetic signatures for risk for high ethanol-preference. 338 DEGs were found to be commonly different between B6, PWK and the average expression of the remaining CC strains within all three regions. The commonly different up-expressed genes were significantly enriched (FDR < 0.001) among genes associated with neuroimmune function. These data compliment findings showing that neuroimmune signaling is key to understanding alcohol use disorder (AUD) and support use of these 8 strains and the highly heterogeneous mouse populations derived from them to identify alcohol-related brain mechanisms and treatment targets.
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Affiliation(s)
- Justin Q. Anderson
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Priscila Darakjian
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Robert Hitzemann
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Denesa R. Lockwood
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Tamara J. Phillips
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Angela R. Ozburn
- Department of Behavioral Neuroscience, Portland Alcohol Research Center, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
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Hitzemann R, Lockwood DR, Ozburn AR, Phillips TJ. On the Use of Heterogeneous Stock Mice to Map Transcriptomes Associated With Excessive Ethanol Consumption. Front Psychiatry 2021; 12:725819. [PMID: 34712155 PMCID: PMC8545898 DOI: 10.3389/fpsyt.2021.725819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/30/2021] [Indexed: 01/11/2023] Open
Abstract
We and many others have noted the advantages of using heterogeneous (HS) animals to map genes and gene networks associated with both behavioral and non-behavioral phenotypes. Importantly, genetically complex Mus musculus crosses provide substantially increased resolution to examine old and new relationships between gene expression and behavior. Here we report on data obtained from two HS populations: the HS/NPT derived from eight inbred laboratory mouse strains and the HS-CC derived from the eight collaborative cross inbred mouse strains that includes three wild-derived strains. Our work has focused on the genes and gene networks associated with risk for excessive ethanol consumption, individual variation in ethanol consumption and the consequences, including escalation, of long-term ethanol consumption. Background data on the development of HS mice is provided, including advantages for the detection of expression quantitative trait loci. Examples are also provided of using HS animals to probe the genes associated with ethanol preference and binge ethanol consumption.
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Affiliation(s)
- Robert Hitzemann
- Department of Behavioral Neuroscience and Portland Alcohol Research Center, Oregon Health & Science University, Portland, OR, United States
| | - Denesa R. Lockwood
- Department of Behavioral Neuroscience and Portland Alcohol Research Center, Oregon Health & Science University, Portland, OR, United States
| | - Angela R. Ozburn
- Department of Behavioral Neuroscience and Portland Alcohol Research Center, Oregon Health & Science University, Portland, OR, United States
- Veterans Affairs Portland Health Care System, Portland, OR, United States
| | - Tamara J. Phillips
- Department of Behavioral Neuroscience and Portland Alcohol Research Center, Oregon Health & Science University, Portland, OR, United States
- Veterans Affairs Portland Health Care System, Portland, OR, United States
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Cheng R, Zheng X, Wang Y, Wang M, Zhou C, Liu J, Zhang Y, Quan F, Liu X. Genome-wide analysis of alternative splicing differences between oocyte and zygote†. Biol Reprod 2021; 102:999-1010. [PMID: 31950147 DOI: 10.1093/biolre/ioaa004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/06/2019] [Accepted: 01/12/2020] [Indexed: 11/14/2022] Open
Abstract
Alternative splicing (AS) of mRNA precursors allows the synthesis of multiple mRNAs from a single primary transcript, significantly expanding the information content and regulatory possibilities of higher eukaryotic genomes. During mammalian development, AS drives certain decisive changes in different physiological processes. As development progresses, the maternal-to-zygotic transition (MZT) will trigger two processes: elimination of a subset of maternal mRNA and transcription of the zygote genome begins. Recent high-throughput technological advancements have facilitated genome-wide AS, whereas its analysis in mouse oocyte transition to the zygote stage has not been reported. We present a high-resolution global analysis of AS transitions and discovered extensive AS transitions between mouse oocyte and zygote. The difference of AS patterns was further confirmed using reverse transcription-polymerase chain reaction analysis. Many genes with specific AS events in mouse oocytes are differentially expressed between oocyte and zygote, but only a few genes with specific AS events in zygote are differentially expressed between oocyte and zygote. We provide a landscape of AS events in mouse oocyte and zygote. Our results advance the understanding of AS transitions during mouse fertilization and its potential functions for MZT and further development.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xiaoman Zheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yingmei Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Mengyun Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Chuan Zhou
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xu Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Saul MC, Philip VM, Reinholdt LG, Chesler EJ. High-Diversity Mouse Populations for Complex Traits. Trends Genet 2019; 35:501-514. [PMID: 31133439 DOI: 10.1016/j.tig.2019.04.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/21/2022]
Abstract
Contemporary mouse genetic reference populations are a powerful platform to discover complex disease mechanisms. Advanced high-diversity mouse populations include the Collaborative Cross (CC) strains, Diversity Outbred (DO) stock, and their isogenic founder strains. When used in systems genetics and integrative genomics analyses, these populations efficiently harnesses known genetic variation for precise and contextualized identification of complex disease mechanisms. Extensive genetic, genomic, and phenotypic data are already available for these high-diversity mouse populations and a growing suite of data analysis tools have been developed to support research on diverse mice. This integrated resource can be used to discover and evaluate disease mechanisms relevant across species.
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Affiliation(s)
- Michael C Saul
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Vivek M Philip
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
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- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA; UNC Chapel Hill, Chapel Hill, NC, USA; SUNY Binghamton, Binghamton, NY, USA; Pittsburgh University, Pittsburgh, PA, USA
| | - Elissa J Chesler
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA.
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Farkas C, Fuentes-Villalobos F, Rebolledo-Jaramillo B, Benavides F, Castro AF, Pincheira R. Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data. BMC Genomics 2019; 20:131. [PMID: 30755158 PMCID: PMC6373082 DOI: 10.1186/s12864-019-5504-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/31/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Historically, gene targeting was first done in embryonic stem cells (ESCs) derived from the 129 family of inbred strains, leading to a mixed background or congenic mice when crossed with C57BL/6 mice. Depending on the number of backcrosses and breeding strategies, genomic segments from 129-derived ESCs can be introgressed into the C57BL/6 genome, establishing a unique genetic makeup that needs characterization in order to obtain valid conclusions from experiments using GEM lines. Currently, SNP genotyping is used to detect the extent of 129-derived ESC genome introgression into C57BL/6 recipients; however, it fails to detect novel/rare variants. RESULTS Here, we present a computational pipeline implemented in the Galaxy platform and in BASH/R script to determine genetic introgression of GEM using next generation sequencing data (NGS), such as whole genome sequencing (WGS), whole exome sequencing (WES) and RNA-Seq. The pipeline includes strategies to uncover variants linked to a targeted locus, genome-wide variant visualization, and the identification of potential modifier genes. Although these methods apply to congenic mice, they can also be used to describe variants fixed by genetic drift. As a proof of principle, we analyzed publicly available RNA-Seq data from five congenic knockout (KO) lines and our own RNA-Seq data from the Sall2 KO line. Additionally, we performed target validation using several genetics approaches. CONCLUSIONS We revealed the impact of the 129-derived ESC genome introgression on gene expression, predicted potential modifier genes, and identified potential phenotypic interference in KO lines. Our results demonstrate that our new approach is an effective method to determine genetic introgression of GEM.
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Affiliation(s)
- C Farkas
- Laboratorio de Transducción de Señales y Cáncer. Departamento de Bioquímica y Biología Molecular. Facultad Cs. Biológicas, Universidad de Concepción, Concepción, Chile
| | - F Fuentes-Villalobos
- Laboratorio de Transducción de Señales y Cáncer. Departamento de Bioquímica y Biología Molecular. Facultad Cs. Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - F Benavides
- Department of Epigenetics and Molecular Carcinogenesis, M.D. Anderson Cancer Center, Smithville, TX, USA
| | - A F Castro
- Laboratorio de Transducción de Señales y Cáncer. Departamento de Bioquímica y Biología Molecular. Facultad Cs. Biológicas, Universidad de Concepción, Concepción, Chile
| | - R Pincheira
- Laboratorio de Transducción de Señales y Cáncer. Departamento de Bioquímica y Biología Molecular. Facultad Cs. Biológicas, Universidad de Concepción, Concepción, Chile.
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Iancu OD, Colville AM, Wilmot B, Searles R, Darakjian P, Zheng C, McWeeney S, Kawane S, Crabbe JC, Metten P, Oberbeck D, Hitzemann R. Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs. Alcohol Clin Exp Res 2018; 42:1454-1465. [PMID: 29786871 DOI: 10.1111/acer.13777] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 05/10/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Transcriptional differences between heterogeneous stock mice and high drinking-in-the-dark selected mouse lines have previously been described based on microarray technology coupled with network-based analysis. The network changes were reproducible in 2 independent selections and largely confined to 2 distinct network modules; in contrast, differential expression appeared more specific to each selected line. This study extends these results by utilizing RNA-Seq technology, allowing evaluation of the relationship between genetic risk and transcription of noncoding RNA (ncRNA); we additionally evaluate sex-specific transcriptional effects of selection. METHODS Naïve mice (N = 24/group and sex) were utilized for gene expression analysis in the ventral striatum; the transcriptome was sequenced with the Illumina HiSeq platform. Differential gene expression and the weighted gene co-expression network analysis were implemented largely as described elsewhere, resulting in the identification of genes that change expression level or (co)variance structure. RESULTS Across both sexes, we detect selection effects on the extracellular matrix and synaptic signaling, although the identity of individual genes varies. A majority of nc RNAs cluster in a single module of relatively low density in both the male and female network. The most strongly differentially expressed transcript in both sexes was Gm22513, a small nuclear RNA with unknown function. Associated with selection, we also found a number of network hubs that change edge strength and connectivity. At the individual gene level, there are many sex-specific effects; however, at the annotation level, results are more concordant. CONCLUSIONS In addition to demonstrating sex-specific effects of selection on the transcriptome, the data point to the involvement of extracellular matrix genes as being associated with the binge drinking phenotype.
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Affiliation(s)
- Ovidiu Dan Iancu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Alex M Colville
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Beth Wilmot
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Robert Searles
- Integrated Genomics Laboratory, Oregon Health & Science University, Portland, Oregon
| | - Priscila Darakjian
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Christina Zheng
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon.,Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Shannon McWeeney
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Sunita Kawane
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - John C Crabbe
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon.,VA Portland Health Care System , Portland, Oregon
| | - Pamela Metten
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon.,VA Portland Health Care System , Portland, Oregon
| | - Denesa Oberbeck
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
| | - Robert Hitzemann
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon
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Suwanmanee T, Ferris MT, Hu P, Gui T, Montgomery SA, Pardo-Manuel de Villena F, Kafri T. Toward Personalized Gene Therapy: Characterizing the Host Genetic Control of Lentiviral-Vector-Mediated Hepatic Gene Delivery. Mol Ther Methods Clin Dev 2017; 5:83-92. [PMID: 28480308 PMCID: PMC5415322 DOI: 10.1016/j.omtm.2017.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/30/2017] [Indexed: 12/21/2022]
Abstract
The success of lentiviral vectors in curing fatal genetic and acquired diseases has opened a new era in human gene therapy. However, variability in the efficacy and safety of this therapeutic approach has been reported in human patients. Consequently, lentiviral-vector-based gene therapy is limited to incurable human diseases, with little understanding of the underlying causes of adverse effects and poor efficacy. To assess the role that host genetic variation has on efficacy of gene therapy, we characterized lentiviral-vector gene therapy within a set of 12 collaborative cross mouse strains. Lentiviral vectors carrying the firefly luciferase cDNA under the control of a liver-specific promoter were administered to female mice, with total-body and hepatic luciferase expression periodically monitored through 41 weeks post-vector administration. Vector copy number per diploid genome in mouse liver and spleen was determined at the end of this study. We identified major strain-specific contributions to overall success of transduction, vector biodistribution, maximum luciferase expression, and the kinetics of luciferase expression throughout the study. Our results highlight the importance of genetic variation on gene-therapeutic efficacy; provide new models with which to more rigorously assess gene therapy approaches; and suggest that redesigning preclinical studies of gene-therapy methodologies might be appropriate.
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Affiliation(s)
- Thipparat Suwanmanee
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Peirong Hu
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tong Gui
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie A. Montgomery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tal Kafri
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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