1
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Johnson EO, Fisher HS, Sullivan KA, Corradin O, Sanchez-Roige S, Gaddis NC, Sami YN, Townsend A, Teixeira Prates E, Pavicic M, Kruse P, Chesler EJ, Palmer AA, Troiani V, Bubier JA, Jacobson DA, Maher BS. An emerging multi-omic understanding of the genetics of opioid addiction. J Clin Invest 2024; 134:e172886. [PMID: 39403933 PMCID: PMC11473141 DOI: 10.1172/jci172886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024] Open
Abstract
Opioid misuse, addiction, and associated overdose deaths remain global public health crises. Despite the tremendous need for pharmacological treatments, current options are limited in number, use, and effectiveness. Fundamental leaps forward in our understanding of the biology driving opioid addiction are needed to guide development of more effective medication-assisted therapies. This Review focuses on the omics-identified biological features associated with opioid addiction. Recent GWAS have begun to identify robust genetic associations, including variants in OPRM1, FURIN, and the gene cluster SCAI/PPP6C/RABEPK. An increasing number of omics studies of postmortem human brain tissue examining biological features (e.g., histone modification and gene expression) across different brain regions have identified broad gene dysregulation associated with overdose death among opioid misusers. Drawn together by meta-analysis and multi-omic systems biology, and informed by model organism studies, key biological pathways enriched for opioid addiction-associated genes are emerging, which include specific receptors (e.g., GABAB receptors, GPCR, and Trk) linked to signaling pathways (e.g., Trk, ERK/MAPK, orexin) that are associated with synaptic plasticity and neuronal signaling. Studies leveraging the agnostic discovery power of omics and placing it within the context of functional neurobiology will propel us toward much-needed, field-changing breakthroughs, including identification of actionable targets for drug development to treat this devastating brain disease.
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Affiliation(s)
- Eric O. Johnson
- GenOmics and Translational Research Center and
- Fellow Program, RTI International, Research Triangle Park, North Carolina, USA
| | | | - Kyle A. Sullivan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Olivia Corradin
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, UCSD, La Jolla, California, USA
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Yasmine N. Sami
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alice Townsend
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Mirko Pavicic
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Peter Kruse
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Abraham A. Palmer
- Department of Psychiatry, UCSD, La Jolla, California, USA
- Institute for Genomic Medicine, UCSD, La Jolla, CA, USA
| | - Vanessa Troiani
- Geisinger College of Health Sciences, Scranton, Pennsylvania, USA
| | | | - Daniel A. Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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2
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Gnatowski ER, Jurmain JL, Dozmorov MG, Wolstenholme JT, Miles MF. Ninein, a candidate gene for ethanol anxiolysis, shows complex exon-specific expression and alternative splicing differences between C57BL/6J and DBA/2J mice. Front Genet 2024; 15:1455616. [PMID: 39323865 PMCID: PMC11422218 DOI: 10.3389/fgene.2024.1455616] [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: 06/27/2024] [Accepted: 08/29/2024] [Indexed: 09/27/2024] Open
Abstract
Ethanol's anxiolytic actions contribute to increased consumption and the development of Alcohol Use Disorder (AUD). Our laboratory previously identified genetic loci contributing to the anxiolytic-like properties of ethanol in BXD recombinant inbred mice, derived from C57BL/6J (B6) and DBA/2J (D2) progenitor strains. That work identified Ninein (Nin) as a candidate gene underlying ethanol's acute anxiolytic-like properties in BXD mice. Nin has a complex exonic content with known alternative splicing events that alter cellular distribution of the NIN protein. We hypothesize that strain-specific differences in Nin alternative splicing contribute to changes in Nin gene expression and B6/D2 strain differences in ethanol anxiolysis. Using quantitative reverse-transcriptase PCR to target specific Nin splice variants, we identified isoform-specific exon expression differences between B6 and D2 mice in prefrontal cortex, nucleus accumbens and amygdala. We extended this analysis using deep RNA sequencing in B6 and D2 nucleus accumbens samples and found that total Nin expression was significantly higher in D2 mice. Furthermore, exon utilization and alternative splicing analyses identified eight differentially utilized exons and significant exon-skipping events between the strains, including three novel splicing events in the 3' end of the Nin gene that were specific to the D2 strain. Additionally, we document multiple single nucleotide polymorphisms in D2 Nin exons that are predicted to have deleterious effects on protein function. Our studies provide the first in-depth analysis of Nin alternative splicing in brain and identify a potential genetic mechanism altering Nin expression and function between B6 and D2 mice, thus possibly contributing to differences in the anxiolytic-like properties of ethanol between these strains. This work adds novel information to our understanding of genetic differences modulating ethanol actions on anxiety that may contribute to the risk for alcohol use disorder.
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Affiliation(s)
- E. R. Gnatowski
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, United States
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, United States
| | - J. L. Jurmain
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, United States
| | - M. G. Dozmorov
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, United States
- Department of Biostatistics, Virginia Commonwealth University, Richmond, United States
| | - J. T. Wolstenholme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, United States
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, United States
| | - M. F. Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, United States
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, United States
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3
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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4
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Kim MJ, Ibrahim MM, Jablonski MM. Deepening insights into cholinergic agents for intraocular pressure reduction: systems genetics, molecular modeling, and in vivo perspectives. Front Mol Biosci 2024; 11:1423351. [PMID: 39130374 PMCID: PMC11310038 DOI: 10.3389/fmolb.2024.1423351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/08/2024] [Indexed: 08/13/2024] Open
Abstract
Parasympathetic activation in the anterior eye segment regulates various physiological functions. This process, mediated by muscarinic acetylcholine receptors, also impacts intraocular pressure (IOP) through the trabecular meshwork. While FDA-approved M3 muscarinic receptor (M3R) agonists exist for IOP reduction, their systemic cholinergic adverse effects pose limitations in clinical use. Therefore, advancing our understanding of the cholinergic system in the anterior segment of the eye is crucial for developing additional IOP-reducing agents with improved safety profiles. Systems genetics analyses were utilized to explore correlations between IOP and the five major muscarinic receptor subtypes. Molecular docking and dynamics simulations were applied to human M3R homology model using a comprehensive set of human M3R ligands and 1,667 FDA-approved or investigational drugs. Lead compounds from the modeling studies were then tested for their IOP-lowering abilities in mice. Systems genetics analyses unveiled positive correlations in mRNA expressions among the five major muscarinic receptor subtypes, with a negative correlation observed only in M3R with IOP. Through modeling studies, rivastigmine and edrophonium emerged as the most optimally suited cholinergic drugs for reducing IOP via a potentially distinct mechanism from pilocarpine or physostigmine. Subsequent animal studies confirmed comparable IOP reductions among rivastigmine, edrophonium, and pilocarpine, with longer durations of action for rivastigmine and edrophonium. Mild cholinergic adverse effects were observed with pilocarpine and rivastigmine but absent with edrophonium. These findings advance ocular therapeutics, suggesting a more nuanced role of the parasympathetic system in the anterior eye segment for reducing IOP than previously thought.
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Affiliation(s)
- Minjae J. Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Mohamed M. Ibrahim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Pharmaceutics, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Monica M. Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States
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5
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Li X, Morel JD, Sulc J, De Masi A, Lalou A, Benegiamo G, Poisson J, Liu Y, Von Alvensleben GVG, Gao AW, Bou Sleiman M, Auwerx J. Systems genetics of metabolic health in the BXD mouse genetic reference population. Cell Syst 2024; 15:497-509.e3. [PMID: 38866010 DOI: 10.1016/j.cels.2024.05.006] [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: 10/11/2023] [Revised: 02/29/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
Susceptibility to metabolic syndrome (MetS) is dependent on genetics, environment, and gene-by-environment interactions, rendering the study of underlying mechanisms challenging. The majority of experiments in model organisms do not incorporate genetic variation and lack specific evaluation criteria for MetS. Here, we derived a continuous metric, the metabolic health score (MHS), based on standard clinical parameters and defined its molecular signatures in the liver and circulation. In human UK Biobank, the MHS associated with MetS status and was predictive of future disease incidence, even in individuals without MetS. Using quantitative trait locus analyses in mice, we found two MHS-associated genetic loci and replicated them in unrelated mouse populations. Through a prioritization scheme in mice and human genetic data, we identified TNKS and MCPH1 as candidates mediating differences in the MHS. Our findings provide insights into the molecular mechanisms sustaining metabolic health across species and uncover likely regulators. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Xiaoxu Li
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jonathan Sulc
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alessia De Masi
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Amélia Lalou
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giorgia Benegiamo
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Johanne Poisson
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yasmine Liu
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giacomo V G Von Alvensleben
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Arwen W Gao
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
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6
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Villani F, Guarracino A, Ward RR, Green T, Emms M, Pravenec M, Prins P, Garrison E, Williams RW, Chen H, Colonna V. Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575041. [PMID: 38260597 PMCID: PMC10802574 DOI: 10.1101/2024.01.10.575041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between Pirl1l1, chromogranin expression, TNF-α levels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.
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Affiliation(s)
- Flavia Villani
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Rachel R Ward
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Tomomi Green
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Madeleine Emms
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Pjotr Prins
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Erik Garrison
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W. Williams
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Vincenza Colonna
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
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7
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Votava JA, John SV, Li Z, Chen S, Fan J, Parks BW. Mining cholesterol genes from thousands of mouse livers identifies aldolase C as a regulator of cholesterol biosynthesis. J Lipid Res 2024; 65:100525. [PMID: 38417553 PMCID: PMC10965479 DOI: 10.1016/j.jlr.2024.100525] [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: 07/11/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/01/2024] Open
Abstract
The availability of genome-wide transcriptomic and proteomic datasets is ever-increasing and often not used beyond initial publication. Here, we applied module-based coexpression network analysis to a comprehensive catalog of 35 mouse genome-wide liver expression datasets (encompassing more than 3800 mice) with the goal of identifying and validating unknown genes involved in cholesterol metabolism. From these 35 datasets, we identified a conserved module of genes enriched with cholesterol biosynthetic genes. Using a systematic approach across the 35 datasets, we identified three genes (Rdh11, Echdc1, and Aldoc) with no known role in cholesterol metabolism. We then performed functional validation studies and show that each gene is capable of regulating cholesterol metabolism. For the glycolytic gene, Aldoc, we demonstrate that it contributes to de novo cholesterol biosynthesis and regulates cholesterol and triglyceride levels in mice. As Aldoc is located within a genome-wide significant genome-wide association studies locus for human plasma cholesterol levels, our studies establish Aldoc as a causal gene within this locus. Through our work, we develop a framework for leveraging mouse genome-wide liver datasets for identifying and validating genes involved in cholesterol metabolism.
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Affiliation(s)
- James A Votava
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Zhonggang Li
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Shuyang Chen
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Jing Fan
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA
| | - Brian W Parks
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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8
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Cousineau CM, Loftus K, Churchill GA, Bridges D. Cross-sectional association between blood cholesterol and calcium levels in genetically diverse strains of mice. FEBS Open Bio 2024; 14:426-433. [PMID: 38129969 PMCID: PMC10909986 DOI: 10.1002/2211-5463.13757] [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: 08/30/2023] [Revised: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023] Open
Abstract
Genetically diverse outbred mice allow for the study of genetic variation in the context of high dietary and environmental control. Using a machine learning approach, we investigated clinical and morphometric factors that associate with serum cholesterol levels in 840 genetically unique Diversity Outbred mice of both sexes (n = 417 male and 423 female), and on both a control chow (% kcals in diet: protein 22%, carbohydrate 62%, fat 16%, no cholesterol) and high fat high sucrose (% kcals in diet: protein 15%, carbohydrate 41%, fat 45%, 0.05% cholesterol). We find expected elevations of cholesterol in male mice, as well as in mice with elevated serum triglycerides and/or fed a high fat high sucrose diet. The third strongest predictor was serum calcium which correlated with serum cholesterol across both diets and sexes (r = 0.39-0.48) in both Diversity Outbred (P = 3.0 × 10-43 ) and BXD (P = 0.005) mice. This is in-line with several human cohort studies which show associations between calcium and cholesterol, and calcium as an independent predictor of cardiovascular events.
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Affiliation(s)
- Cody M. Cousineau
- Department of Nutritional SciencesUniversity of Michigan School of Public HealthAnn ArborMIUSA
| | - Kaelin Loftus
- Department of Nutritional SciencesUniversity of Michigan School of Public HealthAnn ArborMIUSA
| | | | - Dave Bridges
- Department of Nutritional SciencesUniversity of Michigan School of Public HealthAnn ArborMIUSA
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9
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Kim MJ, Kulkarni V, Goode MA, Hernandez J, Graham S, Sivesind TE, Manchadi ML. Utilizing systems genetics to enhance understanding into molecular targets of skin cancer. Exp Dermatol 2024; 33:e15043. [PMID: 38459629 PMCID: PMC11018140 DOI: 10.1111/exd.15043] [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: 12/31/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/10/2024]
Abstract
Despite progress made with immune checkpoint inhibitors and targeted therapies, skin cancer remains a significant public health concern in the United States. The intricacies of the disease, encompassing genetics, immune responses, and external factors, call for a comprehensive approach. Techniques in systems genetics, including transcriptional correlation analysis, functional pathway enrichment analysis, and protein-protein interaction network analysis, prove valuable in deciphering intricate molecular mechanisms and identifying potential diagnostic and therapeutic targets for skin cancer. Recent studies demonstrate the efficacy of these techniques in uncovering molecular processes and pinpointing diagnostic markers for various skin cancer types, highlighting the potential of systems genetics in advancing innovative therapies. While certain limitations exist, such as generalizability and contextualization of external factors, the ongoing progress in AI technologies provides hope in overcoming these challenges. By providing protocols and a practical example involving Braf, we aim to inspire early-career experimental dermatologists to adopt these tools and seamlessly integrate these techniques into their skin cancer research, positioning them at the forefront of innovative approaches in combating this devastating disease.
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Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | | | - Micah A Goode
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Jacob Hernandez
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Sean Graham
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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10
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Sasani TA, Quinlan AR, Harris K. Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice. eLife 2024; 12:RP89096. [PMID: 38381482 PMCID: PMC10942616 DOI: 10.7554/elife.89096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.
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Affiliation(s)
- Thomas A Sasani
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
- Department of Biomedical Informatics, University of UtahSalt Lake CityUnited States
| | - Kelley Harris
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Herbold Computational Biology Program, Fred Hutch Cancer CenterSeattleUnited States
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11
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Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim MJ, He H, Emerson J, Berger AK, Walton DO, Sheppard K, El Kassaby B, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis. Genome Res 2024; 34:145-159. [PMID: 38290977 PMCID: PMC10903950 DOI: 10.1101/gr.278157.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024]
Abstract
Hundreds of inbred mouse strains and intercross populations have been used to characterize the function of genetic variants that contribute to disease. Thousands of disease-relevant traits have been characterized in mice and made publicly available. New strains and populations including consomics, the collaborative cross, expanded BXD, and inbred wild-derived strains add to existing complex disease mouse models, mapping populations, and sensitized backgrounds for engineered mutations. The genome sequences of inbred strains, along with dense genotypes from others, enable integrated analysis of trait-variant associations across populations, but these analyses are hampered by the sparsity of genotypes available. Moreover, the data are not readily interoperable with other resources. To address these limitations, we created a uniformly dense variant resource by harmonizing multiple data sets. Missing genotypes were imputed using the Viterbi algorithm with a data-driven technique that incorporates local phylogenetic information, an approach that is extendable to other model organisms. The result is a web- and programmatically accessible data service called GenomeMUSter, comprising single-nucleotide variants covering 657 strains at 106.8 million segregating sites. Interoperation with phenotype databases, analytic tools, and other resources enable a wealth of applications, including multitrait, multipopulation meta-analysis. We show this in cross-species comparisons of type 2 diabetes and substance use disorder meta-analyses, leveraging mouse data to characterize the likely role of human variant effects in disease. Other applications include refinement of mapped loci and prioritization of strain backgrounds for disease modeling to further unlock extant mouse diversity for genetic and genomic studies in health and disease.
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Affiliation(s)
- Robyn L Ball
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA;
| | - Molly A Bogue
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - David G Ashbrook
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | | | | | - Alexander S Hatoum
- Psychological and Brain Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, USA
- Artificial Intelligence and the Internet of Things Institute, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Matthew J Kim
- University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Hao He
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Jake Emerson
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | | | | | | | | | - Lu Lu
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - John Bluis
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Sejal Desai
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Zhuoqing Fang
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Robert W Williams
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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12
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Yu T, Ji Y, Cui X, Liang N, Wu S, Xiang C, Li Y, Tao H, Xie Y, Zuo H, Wang W, Khan N, Ullah K, Xu F, Zhang Y, Lin C. Novel Pathogenic Mutation of P209L in TRPC6 Gene Causes Adult Focal Segmental Glomerulosclerosis. Biochem Genet 2024:10.1007/s10528-023-10651-y. [PMID: 38315264 DOI: 10.1007/s10528-023-10651-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a leading kidney disease, clinically associated with proteinuria and progressive renal failure. The occurrence of this disease is partly related to gene mutations. We describe a single affected family member who presented with FSGS. We used high-throughput sequencing, sanger sequencing to identify the pathogenic mutations, and a systems genetics analysis in the BXD mice was conducted to explore the genetic regulatory mechanisms of pathogenic genes in the development of FSGS. We identified high urinary protein (++++) and creatinine levels (149 μmol/L) in a 29-year-old male diagnosed with a 5-year history of grade 2 hypertension. Histopathology of the kidney biopsy showed stromal hyperplasia at the glomerular segmental sclerosis and endothelial cell vacuolation degeneration. Whole-exome sequencing followed by Sanger sequencing revealed a heterozygous missense mutation (c.643C > T) in exon 2 of TRPC6, leading to the substitution of arginine with tryptophan at position 215 (p.Arg215Trp). Systems genetics analysis of the 53 BXD mice kidney transcriptomes identified Pygm as the upstream regulator of Trpc6. Those two genes are jointly involved in the regulation of FSGS mainly via Wnt and Hippo signaling pathways. We present a novel variant in the TRPC6 gene that causes FSGS. Moreover, our data suggested TRPC6 works with PYGM, as well as Wnt and Hippo signaling pathways to regulate renal function, which could guide future clinical prevention and targeted treatment for FSGS outcomes.
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Affiliation(s)
- Tianxi Yu
- School of Clinical Medicine, Weifang Medical University, Weifang, 261042, China
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Yongqiang Ji
- Department of Nephrology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Xin Cui
- School of Clinical Medicine, Weifang Medical University, Weifang, 261042, China
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Ning Liang
- School of Clinical Medicine, Weifang Medical University, Weifang, 261042, China
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Shuang Wu
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Chongjun Xiang
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yue Li
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Huiying Tao
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yaqi Xie
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Hongwei Zuo
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
- The 2nd Medical College of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Wenting Wang
- Central Laboratory, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China
| | - Nauman Khan
- Department of Biology, Faculty of Biological and Biomedical Sciences, The University of Haripur, Haripur, KP, Pakistan
| | - Kamran Ullah
- Department of Biology, Faculty of Biological and Biomedical Sciences, The University of Haripur, Haripur, KP, Pakistan
| | - Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yan Zhang
- Department of Nephrology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China.
| | - Chunhua Lin
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000, Shandong, China.
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13
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Xu F, Chen A, Pan S, Wu Y, He H, Han Z, Lu L, Orgil B, Chi X, Yang C, Jia S, Yu C, Mi J. Systems genetics analysis reveals the common genetic basis for pain sensitivity and cognitive function. CNS Neurosci Ther 2024; 30:e14557. [PMID: 38421132 PMCID: PMC10850811 DOI: 10.1111/cns.14557] [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: 07/11/2023] [Revised: 10/31/2023] [Accepted: 11/25/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND There is growing evidence of a strong correlation between pain sensitivity and cognitive function under both physiological and pathological conditions. However, the detailed mechanisms remain largely unknown. In the current study, we sought to explore candidate genes and common molecular mechanisms underlying pain sensitivity and cognitive function with a transcriptome-wide association study using recombinant inbred mice from the BXD family. METHODS The pain sensitivity determined by Hargreaves' paw withdrawal test and cognition-related phenotypes were systematically analyzed in 60 strains of BXD mice and correlated with hippocampus transcriptomes, followed by quantitative trait locus (QTL) mapping and systems genetics analysis. RESULTS The pain sensitivity showed significant variability across the BXD strains and co-varies with cognitive traits. Pain sensitivity correlated hippocampual genes showed a significant involvement in cognition-related pathways, including glutamatergic synapse, and PI3K-Akt signaling pathway. Moreover, QTL mapping identified a genomic region on chromosome 4, potentially regulating the variation of pain sensitivity. Integrative analysis of expression QTL mapping, correlation analysis, and Bayesian network modeling identified Ring finger protein 20 (Rnf20) as the best candidate. Further pathway analysis indicated that Rnf20 may regulate the expression of pain sensitivity and cognitive function through the PI3K-Akt signaling pathway, particularly through interactions with genes Ppp2r2b, Ppp2r5c, Col9a3, Met, Rps6, Tnc, and Kras. CONCLUSIONS Our study demonstrated that pain sensitivity is associated with genetic background and Rnf20-mediated PI3K-Akt signaling may involve in the regulation of pain sensitivity and cognitive functions.
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Affiliation(s)
- Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Anran Chen
- The Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantaiChina
| | - Shuijing Pan
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yingying Wu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Hongjie He
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Zhe Han
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Lu Lu
- University of Tennessee Health Science CenterMemphisTennesseeUSA
| | | | - XiaoDong Chi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Cunhua Yang
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Shushan Jia
- Department of AnesthesiologyYanTai Affiliated Hospital of BinZhou Medical UniversityYantaiChina
| | - Cuicui Yu
- The Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantaiChina
| | - Jia Mi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
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14
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Bajpai AK, Gu Q, Jiao Y, Starlard-Davenport A, Gu W, Quarles LD, Xiao Z, Lu L. Systems genetics and bioinformatics analyses using ESR1-correlated genes identify potential candidates underlying female bone development. Genomics 2024; 116:110769. [PMID: 38141931 PMCID: PMC10811775 DOI: 10.1016/j.ygeno.2023.110769] [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: 07/22/2023] [Revised: 11/14/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Estrogen receptor α (ESR1) is involved in E2 signaling and plays a major role in postmenopausal bone loss. However, the molecular network underlying ESR1 has not been explored. We used systems genetics and bioinformatics to identify important genes associated with Esr1 in postmenopausal bone loss. We identified ~2300 Esr1-coexpressed genes in female BXD bone femur, functional analysis of which revealed 'osteoblast signaling' as the most enriched pathway. PPI network led to the identification of 25 'female bone candidates'. The gene-regulatory analysis revealed RUNX2 as a key TF. ANKRD1 and RUNX2 were significantly different between osteoporosis patients and healthy controls. Sp7, Col1a1 and Pth1r correlated with multiple femur bone phenotypes in BXD mice. miR-3121-3p targeted Csf1, Ankrd1, Sp7 and Runx2. β-estradiol treatment markedly increased the expression of these candidates in mouse osteoblast. Our study revealed that Esr1-correlated genes Ankrd1, Runx2, Csf1 and Sp7 may play important roles in female bone development.
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Affiliation(s)
- Akhilesh K Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Cardiology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Yan Jiao
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Weikuan Gu
- Department of Orthopaedic Surgery and Biomedical Engineering, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Leigh Darryl Quarles
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Zhousheng Xiao
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
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15
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Bajpai AK, Gu Q, Orgil BO, Alberson NR, Towbin JA, Martinez HR, Lu L, Purevjav E. Exploring the Regulation and Function of Rpl3l in the Development of Early-Onset Dilated Cardiomyopathy and Congestive Heart Failure Using Systems Genetics Approach. Genes (Basel) 2023; 15:53. [PMID: 38254943 PMCID: PMC10815855 DOI: 10.3390/genes15010053] [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: 12/05/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cardiomyopathies, diseases affecting the myocardium, are common causes of congestive heart failure (CHF) and sudden cardiac death. Recently, biallelic variants in ribosomal protein L3-like (RPL3L) have been reported to be associated with severe neonatal dilated cardiomyopathy (DCM) and CHF. This study employs a systems genetics approach to gain understanding of the regulatory mechanisms underlying the role of RPL3L in DCM. METHODS Genetic correlation, expression quantitative trait loci (eQTL) mapping, differential expression analysis and comparative functional analysis were performed using cardiac gene expression data from the patients and murine genetic reference populations (GRPs) of BXD mice (recombinant inbred strains from a cross of C57BL/6J and DBA/2J mice). Additionally, immune infiltration analysis was performed to understand the relationship between DCM, immune cells and RPL3L expression. RESULTS Systems genetics analysis identified high expression of Rpl3l mRNA, which ranged from 11.31 to 12.16 across murine GRPs of BXD mice, with an ~1.8-fold difference. Pathways such as "diabetic cardiomyopathy", "focal adhesion", "oxidative phosphorylation" and "DCM" were significantly associated with Rpl3l. eQTL mapping suggested Myl4 (Chr 11) and Sdha (Chr 13) as the upstream regulators of Rpl3l. The mRNA expression of Rpl3l, Myl4 and Sdha was significantly correlated with multiple echocardiography traits in BXD mice. Immune infiltration analysis revealed a significant association of RPL3L and SDHA with seven immune cells (CD4, CD8-naive T cell, CD8 T cell, macrophages, cytotoxic T cell, gamma delta T cell and exhausted T cell) that were also differentially infiltrated between heart samples obtained from DCM patients and normal individuals. CONCLUSIONS RPL3L is highly expressed in the heart tissue of humans and mice. Expression of Rpl3l and its upstream regulators, Myl4 and Sdha, correlate with multiple cardiac function traits in murine GRPs of BXD mice, while RPL3L and SDHA correlate with immune cell infiltration in DCM patient hearts, suggesting important roles for RPL3L in DCM and CHF pathogenesis via immune inflammation, necessitating experimental validations of Myl4 and Sdha in Rpl3l regulation.
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Affiliation(s)
- Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Buyan-Ochir Orgil
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Neely R. Alberson
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Jeffrey A. Towbin
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
- Cardiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hugo R. Martinez
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Enkhsaikhan Purevjav
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
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16
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Yang Y, Zhang M, Zhao Y, Deng T, Zhou X, Qian H, Wang M, Zhang C, Huo Z, Mao Z, Shao Z, Liu M, Yang C, Lin C, Xu F, Tian G, Zhang Y. HOXD8 suppresses renal cell carcinoma growth by upregulating SHMT1 expression. Cancer Sci 2023; 114:4583-4595. [PMID: 37752684 PMCID: PMC10728000 DOI: 10.1111/cas.15982] [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: 04/12/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Amplification of amino acids synthesis is reported to promote tumorigenesis. The serine/glycine biosynthesis pathway is a reversible conversion of serine and glycine catalyzed by cytoplasmic serine hydroxymethyltransferase (SHMT)1 and mitochondrial SHMT2; however, the role of SHTM1 in renal cell carcinoma (RCC) is still unclear. We found that low SHMT1 expression is correlated with poor survival of RCC patients. The in vitro study showed that overexpression of SHMT1 suppressed RCC proliferation and migration. In the mouse tumor model, SHMT1 significantly retarded RCC tumor growth. Furthermore, by gene network analysis, we found several SHMT1-related genes, among which homeobox D8 (HOXD8) was identified as the SHMT1 regulator. Knockdown of HOXD8 decreased SHMT1 expression, resulting in faster RCC growth, and rescued the SHMT1 overexpression-induced cell migration defects. Additionally, ChIP assay found the binding site of HOXD8 to SHMT1 promoter was at the -456~-254 bp region. Taken together, SHMT1 functions as a tumor suppressor in RCC. The transcription factor HOXD8 can promote SHMT1 expression and suppress RCC cell proliferation and migration, which provides new mechanisms of SHMT1 in RCC tumor growth and might be used as a potential therapeutic target candidate for clinical treatment.
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Affiliation(s)
- Yang Yang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Minghui Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yaxuan Zhao
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Tingzhi Deng
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Xiang Zhou
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Hanxu Qian
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Mengxuan Wang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Chuanchuan Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Zhengjin Huo
- The First School of Clinical MedicineBinzhou Medical UniversityYantaiChina
| | - Zijun Mao
- The First School of Clinical MedicineBinzhou Medical UniversityYantaiChina
| | - Zhufeng Shao
- School of PharmacyBinzhou Medical UniversityYantaiChina
| | - Mengxue Liu
- School of PharmacyBinzhou Medical UniversityYantaiChina
| | - Chunhua Yang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Chunhua Lin
- Department of UrologyThe Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantaiChina
| | - Fuyi Xu
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Geng Tian
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yin Zhang
- School of PharmacyBinzhou Medical UniversityYantaiChina
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis, and TreatmentBinzhou Medical UniversityYantaiChina
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17
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Mozhui K, Kim H, Villani F, Haghani A, Sen S, Horvath S. Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits. Epigenetics 2023; 18:2252631. [PMID: 37691384 PMCID: PMC10496549 DOI: 10.1080/15592294.2023.2252631] [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: 05/01/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. Trans-modulated CpGs showed age-dependent changes and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and ageing resulted in a more 'aged methylome' for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analyses identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variations in body size and metabolic traits, and influence CpG methylation and epigenetic ageing that could have an impact on lifespan.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hyeonju Kim
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
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18
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Kim MJ, Martin CA, Kim J, Jablonski MM. Computational methods in glaucoma research: Current status and future outlook. Mol Aspects Med 2023; 94:101222. [PMID: 37925783 PMCID: PMC10842846 DOI: 10.1016/j.mam.2023.101222] [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: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Advancements in computational techniques have transformed glaucoma research, providing a deeper understanding of genetics, disease mechanisms, and potential therapeutic targets. Systems genetics integrates genomic and clinical data, aiding in identifying drug targets, comprehending disease mechanisms, and personalizing treatment strategies for glaucoma. Molecular dynamics simulations offer valuable molecular-level insights into glaucoma-related biomolecule behavior and drug interactions, guiding experimental studies and drug discovery efforts. Artificial intelligence (AI) technologies hold promise in revolutionizing glaucoma research, enhancing disease diagnosis, target identification, and drug candidate selection. The generalized protocols for systems genetics, MD simulations, and AI model development are included as a guide for glaucoma researchers. These computational methods, however, are not separate and work harmoniously together to discover novel ways to combat glaucoma. Ongoing research and progresses in genomics technologies, MD simulations, and AI methodologies project computational methods to become an integral part of glaucoma research in the future.
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Affiliation(s)
- Minjae J Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Cole A Martin
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Jinhwa Kim
- Graduate School of Artificial Intelligence, Graduate School of Metaverse, Department of Management Information Systems, Sogang University, 1 Shinsoo-Dong, Mapo-Gu, Seoul, South Korea.
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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19
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Kim MJ, Kulkarni V, Goode MA, Sivesind TE. Exploring the interactions of antihistamine with retinoic acid receptor beta (RARB) by molecular dynamics simulations and genome-wide meta-analysis. J Mol Graph Model 2023; 124:108539. [PMID: 37331258 PMCID: PMC10529808 DOI: 10.1016/j.jmgm.2023.108539] [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: 02/23/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
Kaposi sarcoma (KS) is one of the most common AIDS-related malignant neoplasms, which can leave lesions on the skin among HIV patients. These lesions can be treated with 9-cis-retinoic acid (9-cis-RA), an endogenous ligand of retinoic acid receptors that has been FDA-approved for treatment of KS. However, topical application of 9-cis-RA can induce several unpleasant side effects, like headache, hyperlipidemia, and nausea. Hence, alternative therapeutics with less side effects are desirable. There are case reports associating over-the-counter antihistamine usage with regression of KS. Antihistamines competitively bind to H1 receptor and block the action of histamine, best known for being released in response to allergens. Furthermore, there are already dozens of antihistamines that are FDA-approved with less side effects than 9-cis-RA. This led our team to conduct a series of in-silico assays to determine whether antihistamines can activate retinoic acid receptors. First, we utilized high-throughput virtual screening and molecular dynamics simulations to model high-affinity interactions between antihistamines and retinoic acid receptor beta (RARβ). We then performed systems genetics analysis to identify a genetic association between H1 receptor itself and molecular pathways involved in KS. Together, these findings advocate for exploration of antihistamines against KS, starting with our two promising hit compounds, bepotastine and hydroxyzine, for experimental validation study in the future.
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Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Sciences Center School of Medicine, Memphis, TN, USA.
| | | | - Micah A Goode
- University of Tennessee Health Sciences Center School of Medicine, Memphis, TN, USA.
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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20
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Zhou Y, Li H, Liu X, Chi X, Gu Z, Cui B, Bergquist J, Wang B, Tian G, Yang C, Xu F, Mi J. The Combination of Quantitative Proteomics and Systems Genetics Analysis Reveals that PTN Is Associated with Sleep-Loss-Induced Cognitive Impairment. J Proteome Res 2023; 22:2936-2949. [PMID: 37611228 DOI: 10.1021/acs.jproteome.3c00269] [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] [Indexed: 08/25/2023]
Abstract
Sleep loss is associated with cognitive dysfunction. However, the detailed mechanisms remain unclear. In this study, we established a para-chlorophenylalanine (PCPA)-induced insomniac mouse model with impaired cognitive function. Mass-spectrometry-based proteomics showed that the expression of 164 proteins was significantly altered in the hippocampus of the PCPA mice. To identify critical regulators among the potential markers, a transcriptome-wide association screening was performed in the BXD mice panel. Among the candidates, the expression of pleiotrophin (Ptn) was significantly associated with cognitive functions, indicating that Ptn-mediates sleep-loss-induced cognitive impairment. Gene co-expression analysis further revealed the potential mechanism by which Ptn mediates insomnia-induced cognitive impairment via the MAPK signaling pathway; that is, the decreased secretion of Ptn induced by insomnia leads to reduced binding to Ptprz1 on the postsynaptic membrane with the activation of the MAPK pathway via Fos and Nr4a1, further leading to the apoptosis of neurons. In addition, Ptn is genetically trans-regulated in the mouse hippocampus and implicated in neurodegenerative diseases in human genome-wide association studies. Our study provides a novel biomarker for insomnia-induced cognitive impairment and a new strategy for seeking neurological biomarkers by the integration of proteomics and systems genetics.
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Affiliation(s)
- Yutong Zhou
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Hui Li
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Xiaoya Liu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Xiaodong Chi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Zhaoxi Gu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Binsen Cui
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Jonas Bergquist
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
- Department of Chemistry-BMC, Analytical Chemistry and Neurochemistry, Uppsala University, Uppsala 75124, Sweden
| | - Binsheng Wang
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Geng Tian
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Chunhua Yang
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Jia Mi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong 264003, China
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21
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Pan L, Cho KS, Wei X, Xu F, Lennikov A, Hu G, Tang J, Guo S, Chen J, Kriukov E, Kyle R, Elzaridi F, Jiang S, Dromel PA, Young M, Baranov P, Do CW, Williams RW, Chen J, Lu L, Chen DF. IGFBPL1 is a master driver of microglia homeostasis and resolution of neuroinflammation in glaucoma and brain tauopathy. Cell Rep 2023; 42:112889. [PMID: 37527036 PMCID: PMC10528709 DOI: 10.1016/j.celrep.2023.112889] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/08/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023] Open
Abstract
Microglia shift toward an inflammatory phenotype during aging that is thought to exacerbate age-related neurodegeneration. The molecular and cellular signals that resolve neuroinflammation post-injury are largely undefined. Here, we exploit systems genetics methods based on the extended BXD murine reference family and identify IGFBPL1 as an upstream cis-regulator of microglia-specific genes to switch off inflammation. IGFBPL1 is expressed by mouse and human microglia, and higher levels of its expression resolve lipopolysaccharide-induced neuroinflammation by resetting the transcriptome signature back to a homeostatic state via IGF1R signaling. Conversely, IGFBPL1 deficiency or selective deletion of IGF1R in microglia shifts these cells to an inflammatory landscape and induces early manifestation of brain tauopathy and retinal neurodegeneration. Therapeutic administration of IGFBPL1 drives pro-homeostatic microglia and prevents glaucomatous neurodegeneration and vision loss in mice. These results identify IGFBPL1 as a master driver of the counter-inflammatory microglial modulator that presents an endogenous resolution of neuroinflammation to prevent neurodegeneration in eye and brain.
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Affiliation(s)
- Li Pan
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; School of Optometry, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Kin-Sang Cho
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Xin Wei
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Anton Lennikov
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Guangan Hu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jing Tang
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA; Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuai Guo
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Julie Chen
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Emil Kriukov
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Robert Kyle
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Farris Elzaridi
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Shuhong Jiang
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Pierre A Dromel
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Michael Young
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Petr Baranov
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Chi-Wai Do
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jianzhu Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Dong Feng Chen
- Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
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22
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Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim M, He H, Emerson J, Berger AK, Walton DO, Sheppard K, Kassaby BE, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multi-trait, multi-population data integration and analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552506. [PMID: 37609331 PMCID: PMC10441370 DOI: 10.1101/2023.08.08.552506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Hundreds of inbred laboratory mouse strains and intercross populations have been used to functionalize genetic variants that contribute to disease. Thousands of disease relevant traits have been characterized in mice and made publicly available. New strains and populations including the Collaborative Cross, expanded BXD and inbred wild-derived strains add to set of complex disease mouse models, genetic mapping resources and sensitized backgrounds against which to evaluate engineered mutations. The genome sequences of many inbred strains, along with dense genotypes from others could allow integrated analysis of trait - variant associations across populations, but these analyses are not feasible due to the sparsity of genotypes available. Moreover, the data are not readily interoperable with other resources. To address these limitations, we created a uniformly dense data resource by harmonizing multiple variant datasets. Missing genotypes were imputed using the Viterbi algorithm with a data-driven technique that incorporates local phylogenetic information, an approach that is extensible to other model organism species. The result is a web- and programmatically-accessible data service called GenomeMUSter ( https://muster.jax.org ), comprising allelic data covering 657 strains at 106.8M segregating sites. Interoperation with phenotype databases, analytic tools and other resources enable a wealth of applications including multi-trait, multi-population meta-analysis. We demonstrate this in a cross-species comparison of the meta-analysis of Type 2 Diabetes and of substance use disorders, resulting in the more specific characterization of the role of human variant effects in light of mouse phenotype data. Other applications include refinement of mapped loci and prioritization of strain backgrounds for disease modeling to further unlock extant mouse diversity for genetic and genomic studies in health and disease.
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23
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Silveira PP, Meaney MJ. Examining the biological mechanisms of human mental disorders resulting from gene-environment interdependence using novel functional genomic approaches. Neurobiol Dis 2023; 178:106008. [PMID: 36690304 DOI: 10.1016/j.nbd.2023.106008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/30/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
We explore how functional genomics approaches that integrate datasets from human and non-human model systems can improve our understanding of the effect of gene-environment interplay on the risk for mental disorders. We start by briefly defining the G-E paradigm and its challenges and then discuss the different levels of regulation of gene expression and the corresponding data existing in humans (genome wide genotyping, transcriptomics, DNA methylation, chromatin modifications, chromosome conformational changes, non-coding RNAs, proteomics and metabolomics), discussing novel approaches to the application of these data in the study of the origins of mental health. Finally, we discuss the multilevel integration of diverse types of data. Advance in the use of functional genomics in the context of a G-E perspective improves the detection of vulnerabilities, informing the development of preventive and therapeutic interventions.
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Affiliation(s)
- Patrícia Pelufo Silveira
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.
| | - Michael J Meaney
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Translational Neuroscience Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), Singapore; Brain - Body Initiative, Agency for Science, Technology and Research (ASTAR), Singapore.
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24
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Bajpai AK, Gu Q, Orgil BO, Xu F, Torres-Rojas C, Zhao W, Chen C, Starlard-Davenport A, Jones B, Lebeche D, Towbin JA, Purevjav E, Lu L, Zhang W. Cardiac copper content and its relationship with heart physiology: Insights based on quantitative genetic and functional analyses using BXD family mice. Front Cardiovasc Med 2023; 10:1089963. [PMID: 36818345 PMCID: PMC9931904 DOI: 10.3389/fcvm.2023.1089963] [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: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background Copper (Cu) is essential for the functioning of various enzymes involved in important cellular and physiological processes. Although critical for normal cardiac function, excessive accumulation, or deficiency of Cu in the myocardium is detrimental to the heart. Fluctuations in cardiac Cu content have been shown to cause cardiac pathologies and imbalance in systemic Cu metabolism. However, the genetic basis underlying cardiac Cu levels and their effects on heart traits remain to be understood. Representing the largest murine genetic reference population, BXD strains have been widely used to explore genotype-phenotype associations and identify quantitative trait loci (QTL) and candidate genes. Methods Cardiac Cu concentration and heart function in BXD strains were measured, followed by QTL mapping. The candidate genes modulating Cu homeostasis in mice hearts were identified using a multi-criteria scoring/filtering approach. Results Significant correlations were identified between cardiac Cu concentration and left ventricular (LV) internal diameter and volumes at end-diastole and end-systole, demonstrating that the BXDs with higher cardiac Cu levels have larger LV chamber. Conversely, cardiac Cu levels negatively correlated with LV posterior wall thickness, suggesting that lower Cu concentration in the heart is associated with LV hypertrophy. Genetic mapping identified six QTLs containing a total of 217 genes, which were further narrowed down to 21 genes that showed a significant association with cardiac Cu content in mice. Among those, Prex1 and Irx3 are the strongest candidates involved in cardiac Cu modulation. Conclusion Cardiac Cu level is significantly correlated with heart chamber size and hypertrophy phenotypes in BXD mice, while being regulated by multiple genes in several QTLs. Prex1 and Irx3 may be involved in modulating Cu metabolism and its downstream effects and warrant further experimental and functional validations.
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Affiliation(s)
- Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,Department of Cardiology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Buyan-Ochir Orgil
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN, United States,Le Bonheur Children’s Hospital, Children’s Foundation Research Institute, Memphis, TN, United States
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai, Shandong, China
| | - Carolina Torres-Rojas
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wenyuan Zhao
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Chen Chen
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Byron Jones
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Djamel Lebeche
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jeffrey A. Towbin
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN, United States,Le Bonheur Children’s Hospital, Children’s Foundation Research Institute, Memphis, TN, United States,Pediatric Cardiology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Enkhsaikhan Purevjav
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN, United States,Le Bonheur Children’s Hospital, Children’s Foundation Research Institute, Memphis, TN, United States
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,*Correspondence: Lu Lu,
| | - Wenjing Zhang
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States,Wenjing Zhang,
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25
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Orgil BO, Xu F, Munkhsaikhan U, Alberson NR, Bajpai AK, Johnson JN, Sun Y, Towbin JA, Lu L, Purevjav E. Echocardiography phenotyping in murine genetic reference population of BXD strains reveals significant QTLs associated with cardiac function and morphology. Physiol Genomics 2023; 55:51-66. [PMID: 36534598 PMCID: PMC9902221 DOI: 10.1152/physiolgenomics.00120.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The genetic reference population of recombinant inbred BXD mice has been derived from crosses between C57BL/6J and DBA/2J strains. The DBA/2J parent exhibits cardiomyopathy phenotypes, whereas C57BL/6J has normal heart. BXD mice are sequenced for studying genetic interactions in cardiomyopathies. The study aimed to assess cardiomyopathy traits in BXDs and investigate the quantitative genetic architecture of those traits. Echocardiography, blood pressure, and cardiomyocyte size parameters obtained from 44 strains of BXD family (n > 5/sex) at 4-5 mo of age were associated with heart transcriptomes and expression quantitative trait loci (eQTL) mapping was performed. More than twofold variance in ejection fraction (EF%), fractional shortening (FS%), left ventricular volumes (LVVols), internal dimensions (LVIDs), mass (LVM), and posterior wall (LVPW) thickness was found among BXDs. In male BXDs, eQTL mapping identified Ndrg4 on chromosome 8 QTL to be positively correlated with LVVol and LVID and negatively associated with cardiomyocyte diameter. In female BXDs, significant QTLs were found on chromosomes 7 and 3 to be associated with LVPW and EF% and FS%, respectively, and Josd2, Dap3, and Tpm3 were predicted as strong candidate genes. Our study found variable cardiovascular traits among BXD strains and identified multiple associated QTLs, suggesting an influence of genetic background on expression of echocardiographic and cardiomyocyte diameter traits. Increased LVVol and reduced EF% and FS% represented dilated cardiomyopathy, whereas increased LV mass and wall thickness indicated hypertrophic cardiomyopathy traits. The BXD family is ideal for identifying candidate genes, causal and modifier, that influence cardiovascular phenotypes.NEW & NOTEWORTHY This study aimed to establish a cardiac phenotype-genotype correlation in murine genetic reference population of BXD RI strains by phenotyping the echocardiography, blood pressure, and cardiomyocyte diameter traits and associating each collected phenotype with genetic background. Our study identified several QTLs and candidate genes that have significant association with cardiac hypertrophy, ventricular dilation, and function including systolic hyperfunction and dysfunction.
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Affiliation(s)
- Buyan-Ochir Orgil
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Undral Munkhsaikhan
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Neely R Alberson
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Jason N Johnson
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Yao Sun
- Division of Cardiovascular Diseases, Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Jeffrey A Towbin
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
- Pediatric Cardiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Enkhsaikhan Purevjav
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
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26
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Distinct gene programs underpinning disease tolerance and resistance in influenza virus infection. Cell Syst 2022; 13:1002-1015.e9. [PMID: 36516834 DOI: 10.1016/j.cels.2022.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/30/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
When challenged with an invading pathogen, the host-defense response is engaged to eliminate the pathogen (resistance) and to maintain health in the presence of the pathogen (disease tolerance). However, the identification of distinct molecular programs underpinning disease tolerance and resistance remained obscure. We exploited transcriptional and physiological monitoring across 33 mouse strains, during in vivo influenza virus infection, to identify two host-defense gene programs-one is associated with hallmarks of disease tolerance and the other with hallmarks of resistance. Both programs constitute generic responses in multiple mouse and human cell types. Our study describes the organizational principles of these programs and validates Arhgdia as a regulator of disease-tolerance states in epithelial cells. We further reveal that the baseline disease-tolerance state in peritoneal macrophages is associated with the pathophysiological response to injury and infection. Our framework provides a paradigm for the understanding of disease tolerance and resistance at the molecular level.
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27
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Esmaeilzadeh AA, Kashian M, Salman HM, Alsaffar MF, Jaber MM, Soltani S, Amiri Manjili D, Ilhan A, Bahrami A, Kastelic JW. Identify Biomarkers and Design Effective Multi-Target Drugs in Ovarian Cancer: Hit Network-Target Sets Model Optimizing. BIOLOGY 2022; 11:1851. [PMID: 36552360 PMCID: PMC9776135 DOI: 10.3390/biology11121851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Epithelial ovarian cancer (EOC) is highly aggressive with poor patient outcomes, and a deeper understanding of ovarian cancer tumorigenesis could help guide future treatment development. We proposed an optimized hit network-target sets model to systematically characterize the underlying pathological mechanisms and intra-tumoral heterogeneity in human ovarian cancer. Using TCGA data, we constructed an epithelial ovarian cancer regulatory network in this study. We use three distinct methods to produce different HNSs for identification of the driver genes/nodes, core modules, and core genes/nodes. Following the creation of the optimized HNS (OHNS) by the integration of DN (driver nodes), CM (core module), and CN (core nodes), the effectiveness of various HNSs was assessed based on the significance of the network topology, control potential, and clinical value. Immunohistochemical (IHC), qRT-PCR, and Western blotting were adopted to measure the expression of hub genes and proteins involved in epithelial ovarian cancer (EOC). We discovered that the OHNS has two key advantages: the network's central location and controllability. It also plays a significant role in the illness network due to its wide range of capabilities. The OHNS and clinical samples revealed the endometrial cancer signaling, and the PI3K/AKT, NER, and BMP pathways. MUC16, FOXA1, FBXL2, ARID1A, COX15, COX17, SCO1, SCO2, NDUFA4L2, NDUFA, and PTEN hub genes were predicted and may serve as potential candidates for new treatments and biomarkers for EOC. This research can aid in better capturing the disease progression, the creation of potent multi-target medications, and the direction of the therapeutic community in the optimization of effective treatment regimens by various research objectives in cancer treatment.
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Affiliation(s)
| | - Mahdis Kashian
- Department of Obstetrics and Gynecology, Medical College of Iran University, Tehran 14535, Iran;
| | - Hayder Mahmood Salman
- Department of Computer Science, Al-Turath University College Al Mansour, Baghdad 10011, Iraq;
| | - Marwa Fadhil Alsaffar
- Medical Laboratory Techniques Department, AL-Mustaqbal University College, Hillah 51001, Iraq;
| | - Mustafa Musa Jaber
- Computer Techniques Engineering Department, Dijlah University College, Baghdad 00964, Iraq;
- Computer Techniques Engineering Department, Al-Farahidi University, Baghdad 10011, Iraq
| | - Siamak Soltani
- Department of Forensic Medicine, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran;
| | - Danial Amiri Manjili
- Department of Infectious Disease, School of Medicine, Babol University of Medical Sciences, Babol 47414, Iran
| | - Ahmet Ilhan
- Department of Medical Biochemistry, Faculty of Medicine, Cukurova University, Adana 01330, Turkey
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 1417643184, Iran;
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, 80333 Munich, Germany
| | - John W. Kastelic
- Department of Health, University of Calgary, Calgary, AB T2N 1N4, Canada;
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28
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Hu W, Liu J, Hu Y, Xu Q, Deng T, Wei M, Lu L, Mi J, Bergquist J, Xu F, Tian G. Transcriptome-wide association study reveals cholesterol metabolism gene Lpl is a key regulator of cognitive dysfunction. Front Mol Neurosci 2022; 15:1044022. [PMID: 36590920 PMCID: PMC9798092 DOI: 10.3389/fnmol.2022.1044022] [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: 09/14/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022] Open
Abstract
Cholesterol metabolism in the brain plays a crucial role in normal physiological function, and its aberrations are associated with cognitive dysfunction. The present study aimed to determine which cholesterol-related genes play a vital role in cognitive dysfunction and to dissect its underlying molecular mechanisms using a systems genetics approach in the BXD mice family. We first systematically analyzed the association of expression of 280 hippocampal genes related to cholesterol metabolism with cognition-related traits and identified lipoprotein lipase (Lpl) as a critical regulator. This was further confirmed by phenome-wide association studies that indicate Lpl associated with hippocampus volume residuals and anxiety-related traits. By performing expression quantitative trait locus mapping, we demonstrate that Lpl is strongly cis-regulated in the BXD hippocampus. We also identified ∼3,300 genes significantly (p < 0.05) correlated with the Lpl expression. Those genes are mainly involved in the regulation of neuron-related traits through the MAPK signaling pathway, axon guidance, synaptic vesicle cycle, and NF-kappa B signaling pathway. Furthermore, a protein-protein interaction network analysis identified several direct interactors of Lpl, including Rab3a, Akt1, Igf1, Crp, and Lrp1, which indicates that Lpl involves in the regulation of cognitive dysfunction through Rab3a-mediated synaptic vesicle cycle and Akt1/Igf1/Crp/Lrp1-mediated MAPK signaling pathway. Our findings demonstrate the importance of the Lpl, among the cholesterol-related genes, in regulating cognitive dysfunction and highlighting the potential signaling pathways, which may serve as novel therapeutic targets for the treatment of cognitive dysfunction.
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Affiliation(s)
- Wei Hu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China,Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Jian Liu
- Department of Plastic Surgery, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China,Jinan Clinical Research Center for Tissue Engineering Skin Regeneration and Wound Repair, Jinan, Shandong, China
| | - Yaorui Hu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Qingling Xu
- Department of Ultrasound, Yantai Affiliated Hospital, Binzhou Medical University, Yantai, Shandong, China
| | - Tingzhi Deng
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Mengna Wei
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jia Mi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Jonas Bergquist
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China,Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden,*Correspondence: Jonas Bergquist,
| | - Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China,Fuyi Xu,
| | - Geng Tian
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China,Geng Tian,
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Bagley JR, Bailey LS, Gagnon LH, He H, Philip VM, Reinholdt LG, Tarantino LM, Chesler EJ, Jentsch JD. Behavioral phenotypes revealed during reversal learning are linked with novel genetic loci in diversity outbred mice. ADDICTION NEUROSCIENCE 2022; 4:100045. [PMID: 36714272 PMCID: PMC9879139 DOI: 10.1016/j.addicn.2022.100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Impulsive behavior and impulsivity are heritable phenotypes that are strongly associated with risk for substance use disorders. Identifying the neurogenetic mechanisms that influence impulsivity may also reveal novel biological insights into addiction vulnerability. Our past studies using the BXD and Collaborative Cross (CC) recombinant inbred mouse panels have revealed that behavioral indicators of impulsivity measured in a reversal-learning task are heritable and are genetically correlated with aspects of intravenous cocaine self-administration. Genome-wide linkage studies in the BXD panel revealed a quantitative trait locus (QTL) on chromosome 10, but we expect to identify additional QTL by testing in a population with more genetic diversity. To this end, we turned to Diversity Outbred (DO) mice; 392 DO mice (156 males, 236 females) were phenotyped using the same reversal learning test utilized previously. Our primary indicator of impulsive responding, a measure that isolates the relative difficulty mice have with reaching performance criteria under reversal conditions, revealed a genome-wide significant QTL on chromosome 7 (max LOD score = 8.73, genome-wide corrected p<0.05). A measure of premature responding akin to that implemented in the 5-choice serial reaction time task yielded a suggestive QTL on chromosome 17 (max LOD score = 9.14, genome-wide corrected <0.1). Candidate genes were prioritized (2900076A07Rik, Wdr73 and Zscan2) based upon expression QTL data we collected in DO and CC mice and analyses using publicly available gene expression and phenotype databases. These findings may advance understanding of the genetics that drive impulsive behavior and enhance risk for substance use disorders.
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Affiliation(s)
- Jared R. Bagley
- Department of Psychology, Binghamton University, Binghamton, NY, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
| | - Lauren S. Bailey
- Department of Psychology, Binghamton University, Binghamton, NY, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
| | - Leona H. Gagnon
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Hao He
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Vivek M. Philip
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Laura G. Reinholdt
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Lisa M. Tarantino
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Elissa J. Chesler
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - James D. Jentsch
- Department of Psychology, Binghamton University, Binghamton, NY, USA
- Center for Systems Neurogenetics of Addiction at The Jackson Laboratory, Bar Harbor, ME, USA
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30
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Sleiman MB, Roy S, Gao AW, Sadler MC, von Alvensleben GVG, Li H, Sen S, Harrison DE, Nelson JF, Strong R, Miller RA, Kutalik Z, Williams RW, Auwerx J. Sex- and age-dependent genetics of longevity in a heterogeneous mouse population. Science 2022; 377:eabo3191. [PMID: 36173858 PMCID: PMC9905652 DOI: 10.1126/science.abo3191] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DNA variants that modulate life span provide insight into determinants of health, disease, and aging. Through analyses in the UM-HET3 mice of the Interventions Testing Program (ITP), we detected a sex-independent quantitative trait locus (QTL) on chromosome 12 and identified sex-specific QTLs, some of which we detected only in older mice. Similar relations between life history and longevity were uncovered in mice and humans, underscoring the importance of early access to nutrients and early growth. We identified common age- and sex-specific genetic effects on gene expression that we integrated with model organism and human data to create a hypothesis-building interactive resource of prioritized longevity and body weight genes. Finally, we validated Hipk1, Ddost, Hspg2, Fgd6, and Pdk1 as conserved longevity genes using Caenorhabditis elegans life-span experiments.
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Affiliation(s)
- Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center (UTHSC), Memphis, TN 38163, USA
| | - Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Marie C. Sadler
- Institute of Primary Care and Public Health (Unisante), University of Lausanne, Lausanne 1011, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Giacomo V. G. von Alvensleben
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Hao Li
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | | | - James F. Nelson
- Barshop Center for Longevity Studies at the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Randy Strong
- Barshop Center for Longevity Studies at the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- South Texas Veterans Healthcare System, San Antonio, TX 78229, USA
| | - Richard A. Miller
- Department of Pathology, University of Michigan Geriatrics Center, Ann Arbor, MI 48109-2200, USA
| | - Zoltán Kutalik
- Institute of Primary Care and Public Health (Unisante), University of Lausanne, Lausanne 1011, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center (UTHSC), Memphis, TN 38163, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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31
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Jagadapillai R, Qiu X, Ojha K, Li Z, El-Baz A, Zou S, Gozal E, Barnes GN. Potential Cross Talk between Autism Risk Genes and Neurovascular Molecules: A Pilot Study on Impact of Blood Brain Barrier Integrity. Cells 2022; 11:2211. [PMID: 35883654 PMCID: PMC9315816 DOI: 10.3390/cells11142211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/10/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a common pediatric neurobiological disorder with up to 80% of genetic etiologies. Systems biology approaches may make it possible to test novel therapeutic strategies targeting molecular pathways to alleviate ASD symptoms. A clinical database of autism subjects was queried for individuals with a copy number variation (CNV) on microarray, Vineland, and Parent Concern Questionnaire scores. Pathway analyses of genes from pathogenic CNVs yielded 659 genes whose protein-protein interactions and mRNA expression mapped 121 genes with maximal antenatal expression in 12 brain regions. A Research Domain Criteria (RDoC)-derived neural circuits map revealed significant differences in anxiety, motor, and activities of daily living skills scores between altered CNV genes and normal microarrays subjects, involving Positive Valence (reward), Cognition (IQ), and Social Processes. Vascular signaling was identified as a biological process that may influence these neural circuits. Neuroinflammation, microglial activation, iNOS and 3-nitrotyrosine increase in the brain of Semaphorin 3F- Neuropilin 2 (Sema 3F-NRP2) KO, an ASD mouse model, agree with previous reports in the brain of ASD individuals. Signs of platelet deposition, activation, release of serotonin, and albumin leakage in ASD-relevant brain regions suggest possible blood brain barrier (BBB) deficits. Disruption of neurovascular signaling and BBB with neuroinflammation may mediate causative pathophysiology in some ASD subgroups. Although preliminary, these data demonstrate the potential for developing novel therapeutic strategies based on clinically derived data, genomics, cognitive neuroscience, and basic neuroscience methods.
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Affiliation(s)
- Rekha Jagadapillai
- Department of Neurology, Pediatric Research Institute, Louisville, KY 40202, USA; (R.J.); (X.Q.); (K.O.)
- University of Louisville Autism Center, Louisville, KY 40217, USA
| | - Xiaolu Qiu
- Department of Neurology, Pediatric Research Institute, Louisville, KY 40202, USA; (R.J.); (X.Q.); (K.O.)
- University of Louisville Autism Center, Louisville, KY 40217, USA
- Department of Pediatrics, Pediatric Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Child Health, Jiangxi Provincial Children’s Hospital, Donghu District, Nanchang 330006, China;
| | - Kshama Ojha
- Department of Neurology, Pediatric Research Institute, Louisville, KY 40202, USA; (R.J.); (X.Q.); (K.O.)
- University of Louisville Autism Center, Louisville, KY 40217, USA
| | - Zhu Li
- Department of Neurology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
| | - Ayman El-Baz
- Department of Bioengineering, University of Louisville Speed School, Louisville, KY 40292, USA;
| | - Shipu Zou
- Department of Child Health, Jiangxi Provincial Children’s Hospital, Donghu District, Nanchang 330006, China;
| | - Evelyne Gozal
- Department of Pediatrics, Pediatric Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Gregory N. Barnes
- Department of Neurology, Pediatric Research Institute, Louisville, KY 40202, USA; (R.J.); (X.Q.); (K.O.)
- University of Louisville Autism Center, Louisville, KY 40217, USA
- Department of Pediatrics, Pediatric Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
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Bagley JR, Khan AH, Smith DJ, Jentsch JD. Extreme phenotypic diversity in operant response to intravenous cocaine or saline infusion in the hybrid mouse diversity panel. Addict Biol 2022; 27:e13162. [PMID: 35470554 PMCID: PMC9870574 DOI: 10.1111/adb.13162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 01/26/2023]
Abstract
Cocaine self-administration is a complexly determined trait, with a substantial proportion of individual differences being determined by genetic variation. However, the relevant genetic variants that drive heritable differences in cocaine use remain undiscovered. Cocaine intravenous self-administration (IVSA) procedures in laboratory animals provide opportunities to prospectively investigate neurogenetic influences on the acquisition of voluntary cocaine use. Here, we provide information on cocaine (or saline-as a control) IVSA in 84 members of the hybrid mouse diversity panel (HMDP), an array of genetically distinct classical or recombinant inbred strains. We found cocaine IVSA to be substantially heritable in this population, with strain-level intake ranging for near 0 to >25 mg/kg/session. Though saline IVSA was also found to be heritable, a modest genetic correlation between cocaine and saline IVSA indicates that operant responding for the cocaine reinforcer was influenced, at least in part, by unique genetic variants. Genome-wide association studies (GWAS) of infusions earned in cocaine and saline groups revealed significant quantitative trait loci (QTL) on Chromosomes 3 and 14 for cocaine, but not saline, IVSA. Positional candidates were further prioritized through use of bulk RNA sequencing data that revealed genes with cis-eQTL and genetic correlation to number of infusions. Additionally, these data identify reference strains with extreme cocaine IVSA phenotypes, revealing them as polygenic models of risk and resilience to cocaine reinforcement. This work is part of an ongoing effort to characterize genetic variation that moderates cocaine IVSA that may, in turn, provide a more comprehensive understanding of cocaine risk genetics and neurobiology.
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Affiliation(s)
- Jared R. Bagley
- Department of Psychology, Binghamton University, Binghamton, New York, USA
| | - Arshad H. Khan
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA
| | - Desmond J. Smith
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA
| | - James D. Jentsch
- Department of Psychology, Binghamton University, Binghamton, New York, USA
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33
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Neuner SM, Telpoukhovskaia M, Menon V, O'Connell KMS, Hohman TJ, Kaczorowski CC. Translational approaches to understanding resilience to Alzheimer's disease. Trends Neurosci 2022; 45:369-383. [PMID: 35307206 PMCID: PMC9035083 DOI: 10.1016/j.tins.2022.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/07/2022] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
Individuals who maintain cognitive function despite high levels of Alzheimer's disease (AD)-associated pathology are said to be 'resilient' to AD. Identifying mechanisms underlying resilience represents an exciting therapeutic opportunity. Human studies have identified a number of molecular and genetic factors associated with resilience, but the complexity of these cohorts prohibits a complete understanding of which factors are causal or simply correlated with resilience. Genetically and phenotypically diverse mouse models of AD provide new and translationally relevant opportunities to identify and prioritize new resilience mechanisms for further cross-species investigation. This review will discuss insights into resilience gained from both human and animal studies and highlight future approaches that may help translate these insights into therapeutics designed to prevent or delay AD-related dementia.
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Affiliation(s)
- Sarah M Neuner
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kristen M S O'Connell
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Tufts University, School of Medicine, Graduate School of Biomedical Sciences, Boston, MA 02111, USA; The University of Maine, Graduate School of Biomedical Science and Engineering, Orono, ME 04469, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Catherine C Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Tufts University, School of Medicine, Graduate School of Biomedical Sciences, Boston, MA 02111, USA; The University of Maine, Graduate School of Biomedical Science and Engineering, Orono, ME 04469, USA.
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34
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Sasani TA, Ashbrook DG, Beichman AC, Lu L, Palmer AA, Williams RW, Pritchard JK, Harris K. A natural mutator allele shapes mutation spectrum variation in mice. Nature 2022; 605:497-502. [PMID: 35545679 PMCID: PMC9272728 DOI: 10.1038/s41586-022-04701-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
Although germline mutation rates and spectra can vary within and between species, common genetic modifiers of the mutation rate have not been identified in nature1. Here we searched for loci that influence germline mutagenesis using a uniquely powerful resource: a panel of recombinant inbred mouse lines known as the BXD, descended from the laboratory strains C57BL/6J (B haplotype) and DBA/2J (D haplotype). Each BXD lineage has been maintained by brother-sister mating in the near absence of natural selection, accumulating de novo mutations for up to 50 years on a known genetic background that is a unique linear mosaic of B and D haplotypes2. We show that mice inheriting D haplotypes at a quantitative trait locus on chromosome 4 accumulate C>A germline mutations at a 50% higher rate than those inheriting B haplotypes, primarily owing to the activity of a C>A-dominated mutational signature known as SBS18. The B and D quantitative trait locus haplotypes encode different alleles of Mutyh, a DNA repair gene that underlies the heritable cancer predisposition syndrome that causes colorectal tumors with a high SBS18 mutation load3,4. Both B and D Mutyh alleles are present in wild populations of Mus musculus domesticus, providing evidence that common genetic variation modulates germline mutagenesis in a model mammalian species.
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Affiliation(s)
- Thomas A Sasani
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David G Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Computational Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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35
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Mozhui K, Lu AT, Li CZ, Haghani A, Sandoval-Sierra JV, Wu Y, Williams RW, Horvath S. Genetic loci and metabolic states associated with murine epigenetic aging. eLife 2022; 11:e75244. [PMID: 35389339 PMCID: PMC9049972 DOI: 10.7554/elife.75244] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
Changes in DNA methylation (DNAm) are linked to aging. Here, we profile highly conserved CpGs in 339 predominantly female mice belonging to the BXD family for which we have deep longevity and genomic data. We use a 'pan-mammalian' microarray that provides a common platform for assaying the methylome across mammalian clades. We computed epigenetic clocks and tested associations with DNAm entropy, diet, weight, metabolic traits, and genetic variation. We describe the multifactorial variance of methylation at these CpGs and show that high-fat diet augments the age-related changes. Entropy increases with age. The progression to disorder, particularly at CpGs that gain methylation over time, was predictive of genotype-dependent life expectancy. The longer-lived BXD strains had comparatively lower entropy at a given age. We identified two genetic loci that modulate epigenetic age acceleration (EAA): one on chromosome (Chr) 11 that encompasses the Erbb2/Her2 oncogenic region, and the other on Chr19 that contains a cytochrome P450 cluster. Both loci harbor genes associated with EAA in humans, including STXBP4, NKX2-3, and CUTC. Transcriptome and proteome analyses revealed correlations with oxidation-reduction, metabolic, and immune response pathways. Our results highlight concordant loci for EAA in humans and mice, and demonstrate a tight coupling between the metabolic state and epigenetic aging.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los AngelesLos AngelesUnited States
| | - Caesar Z Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los AngelesLos AngelesUnited States
| | - Amin Haghani
- Department of Biostatistics, Fielding School of Public Health, University of California Los AngelesLos AngelesUnited States
| | - Jose Vladimir Sandoval-Sierra
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
| | - Yibo Wu
- YCI Laboratory for Next-Generation Proteomics, RIKEN Center for Integrative Medical SciencesYokohamaJapan
- University of GenevaGenevaSwitzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of MedicineMemphisUnited States
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los AngelesLos AngelesUnited States
- Department of Biostatistics, Fielding School of Public Health, University of California Los AngelesLos AngelesUnited States
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36
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Senko AN, Overall RW, Silhavy J, Mlejnek P, Malínská H, Hüttl M, Marková I, Fabel KS, Lu L, Stuchlik A, Williams RW, Pravenec M, Kempermann G. Systems genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose. PLoS Genet 2022; 18:e1009638. [PMID: 35377872 PMCID: PMC9060359 DOI: 10.1371/journal.pgen.1009638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 05/02/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Neurogenesis in the adult hippocampus contributes to learning and memory in the healthy brain but is dysregulated in metabolic and neurodegenerative diseases. The molecular relationships between neural stem cell activity, adult neurogenesis, and global metabolism are largely unknown. Here we applied unbiased systems genetics methods to quantify genetic covariation among adult neurogenesis and metabolic phenotypes in peripheral tissues of a genetically diverse family of rat strains, derived from a cross between the spontaneously hypertensive (SHR/OlaIpcv) strain and Brown Norway (BN-Lx/Cub). The HXB/BXH family is a very well established model to dissect genetic variants that modulate metabolic and cardiovascular diseases and we have accumulated deep phenome and transcriptome data in a FAIR-compliant resource for systematic and integrative analyses. Here we measured rates of precursor cell proliferation, survival of new neurons, and gene expression in the hippocampus of the entire HXB/BXH family, including both parents. These data were combined with published metabolic phenotypes to detect a neurometabolic quantitative trait locus (QTL) for serum glucose and neuronal survival on Chromosome 16: 62.1-66.3 Mb. We subsequently fine-mapped the key phenotype to a locus that includes the Telo2-interacting protein 2 gene (Tti2)-a chaperone that modulates the activity and stability of PIKK kinases. To verify the hypothesis that differences in neurogenesis and glucose levels are caused by a polymorphism in Tti2, we generated a targeted frameshift mutation on the SHR/OlaIpcv background. Heterozygous SHR-Tti2+/- mutants had lower rates of hippocampal neurogenesis and hallmarks of dysglycemia compared to wild-type littermates. Our findings highlight Tti2 as a causal genetic link between glucose metabolism and structural brain plasticity. In humans, more than 800 genomic variants are linked to TTI2 expression, seven of which have associations to protein and blood stem cell factor concentrations, blood pressure and frontotemporal dementia.
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Affiliation(s)
- Anna N. Senko
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Rupert W. Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Malínská
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Hüttl
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Irena Marková
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Klaus S. Fabel
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Ales Stuchlik
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
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37
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Yang L, Zhang W, Li M, Dam J, Huang K, Wang Y, Qiu Z, Sun T, Chen P, Zhang Z, Zhang W. Evaluation of the Prognostic Relevance of Differential Claudin Gene Expression Highlights Claudin-4 as Being Suppressed by TGFβ1 Inhibitor in Colorectal Cancer. Front Genet 2022; 13:783016. [PMID: 35281827 PMCID: PMC8907593 DOI: 10.3389/fgene.2022.783016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Claudins (CLDNs) are a family of closely related transmembrane proteins that have been linked to oncogenic transformation and metastasis across a range of cancers, suggesting that they may be valuable diagnostic and/or prognostic biomarkers that can be used to evaluate patient outcomes. However, CLDN expression patterns associated with colorectal cancer (CRC) remain to be defined.Methods: The mRNA levels of 21 different CLDN family genes were assessed across 20 tumor types using the Oncomine database. Correlations between these genes and patient clinical outcomes, immune cell infiltration, clinicopathological staging, lymph node metastasis, and mutational status were analyzed using the GEPIA, UALCAN, Human Protein Atlas, Tumor Immune Estimation Resource, STRING, Genenetwork, cBioportal, and DAVID databases in an effort to clarify the potential functional roles of different CLDN protein in CRC. Molecular docking analyses were used to probe potential interactions between CLDN4 and TGFβ1. Levels of CLDN4 and CLDN11 mRNA expression in clinical CRC patient samples and in the HT29 and HCT116 cell lines were assessed via qPCR. CLDN4 expression levels in these 2 cell lines were additionally assessed following TGFβ1 inhibitor treatment.Results: These analyses revealed that COAD and READ tissues exhibited the upregulation of CLDN1, CLDN2, CLDN3, CLDN4, CLDN7, and CLDN12 as well as the downregulation of CLDN5 and CLDN11 relative to control tissues. Higher CLDN11 and CLDN14 expression as well as lower CLDN23 mRNA levels were associated with poorer overall survival (OS) outcomes. Moreover, CLDN2 and CLDN3 or CLDN11 mRNA levels were significantly associated with lymph node metastatic progression in COAD or READ lower in COAD and READ tissues. A positive correlation between the expression of CLDN11 and predicted macrophage, dendritic cell, and CD4+ T cell infiltration was identified in CRC, with CLDN12 expression further being positively correlated with CD4+ T cell infiltration whereas a negative correlation was observed between such infiltration and the expression of CLDN3 and CLDN15. A positive correlation between CLDN1, CLDN16, and neutrophil infiltration was additionally detected, whereas neutrophil levels were negatively correlated with the expression of CLDN3 and CLDN15. Molecular docking suggested that CLDN4 was able to directly bind via hydrogen bond with TGFβ1. Relative to paracancerous tissues, clinical CRC tumor tissue samples exhibited CLDN4 and CLDN11 upregulation and downregulation, respectively. LY364947 was able to suppress the expression of CLDN4 in both the HT29 and HCT116 cell lines.Conclusion: Together, these results suggest that the expression of different CLDN family genes is closely associated with CRC tumor clinicopathological staging and immune cell infiltration. Moreover, CLDN4 expression is closely associated with TGFβ1 in CRC, suggesting that it and other CLDN family members may represent viable targets for antitumor therapeutic intervention.
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Affiliation(s)
- Linqi Yang
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Wenqi Zhang
- Department of Hematology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Meng Li
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Jinxi Dam
- College of Natural Science, Michigan State University, East Lansing, MI, United States
| | - Kai Huang
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yihan Wang
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Zhicong Qiu
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Tao Sun
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Pingping Chen
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
- *Correspondence: Wei Zhang, ; Pingping Chen, ; Zhenduo Zhang,
| | - Zhenduo Zhang
- Shijiazhuang People’s Hospital, Shijiazhuang, China
- *Correspondence: Wei Zhang, ; Pingping Chen, ; Zhenduo Zhang,
| | - Wei Zhang
- Department of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang, China
- *Correspondence: Wei Zhang, ; Pingping Chen, ; Zhenduo Zhang,
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Williams EG, Pfister N, Roy S, Statzer C, Haverty J, Ingels J, Bohl C, Hasan M, Čuklina J, Bühlmann P, Zamboni N, Lu L, Ewald CY, Williams RW, Aebersold R. Multiomic profiling of the liver across diets and age in a diverse mouse population. Cell Syst 2022; 13:43-57.e6. [PMID: 34666007 PMCID: PMC8776606 DOI: 10.1016/j.cels.2021.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 01/21/2023]
Abstract
We profiled the liver transcriptome, proteome, and metabolome in 347 individuals from 58 isogenic strains of the BXD mouse population across age (7 to 24 months) and diet (low or high fat) to link molecular variations to metabolic traits. Several hundred genes are affected by diet and/or age at the transcript and protein levels. Orthologs of two aging-associated genes, St7 and Ctsd, were knocked down in C. elegans, reducing longevity in wild-type and mutant long-lived strains. The multiomics data were analyzed as segregating gene networks according to each independent variable, providing causal insight into dietary and aging effects. Candidates were cross-examined in an independent diversity outbred mouse liver dataset segregating for similar diets, with ∼80%-90% of diet-related candidate genes found in common across datasets. Together, we have developed a large multiomics resource for multivariate analysis of complex traits and demonstrate a methodology for moving from observational associations to causal connections.
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Affiliation(s)
- Evan G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Niklas Pfister
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Suheeta Roy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Cyril Statzer
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Jack Haverty
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jesse Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Casey Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Moaraj Hasan
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Jelena Čuklina
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Peter Bühlmann
- Department of Mathematics, Seminar for Statistics, ETH Zürich, Zurich, Switzerland
| | - Nicola Zamboni
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Collin Y Ewald
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland; Faculty of Science, University of Zürich, Zurich, Switzerland
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39
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Dietrich P, Alli S, Mulligan MK, Cox R, Ashbrook DG, Williams RW, Dragatsis I. Identification of cyclin D1 as a major modulator of 3-nitropropionic acid-induced striatal neurodegeneration. Neurobiol Dis 2022; 162:105581. [PMID: 34871739 PMCID: PMC8717869 DOI: 10.1016/j.nbd.2021.105581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/14/2021] [Accepted: 12/02/2021] [Indexed: 01/03/2023] Open
Abstract
Mitochondria dysfunction occurs in the aging brain as well as in several neurodegenerative disorders and predisposes neuronal cells to enhanced sensitivity to neurotoxins. 3-nitropropionic acid (3-NP) is a naturally occurring plant and fungal neurotoxin that causes neurodegeneration predominantly in the striatum by irreversibly inhibiting the tricarboxylic acid respiratory chain enzyme, succinate dehydrogenase (SDH), the main constituent of the mitochondria respiratory chain complex II. Significantly, although 3-NP-induced inhibition of SDH occurs in all brain regions, neurodegeneration occurs primarily and almost exclusively in the striatum for reasons still not understood. In rodents, 3-NP-induced striatal neurodegeneration depends on the strain background suggesting that genetic differences among genotypes modulate toxicant variability and mechanisms that underlie 3-NP-induced neuronal cell death. Using the large BXD family of recombinant inbred (RI) strains we demonstrate that variants in Ccnd1 - the gene encoding cyclin D1 - of the DBA/2 J parent underlie the resistance to 3-NP-induced striatal neurodegeneration. In contrast, the Ccnd1 variant inherited from the widely used C57BL/6 J parental strain confers sensitivity. Given that cellular stress triggers induction of cyclin D1 expression followed by cell-cycle re-entry and consequent neuronal cell death, we sought to determine if the C57BL/6 J and DBA/2 J Ccnd1 variants are differentially modulated in response to 3-NP. We confirm that 3-NP induces cyclin D1 expression in striatal neuronal cells of C57BL/6 J, but this response is blunted in the DBA/2 J. We further show that striatal-specific alternative processing of a highly conserved 3'UTR negative regulatory region of Ccnd1 co-segregates with the C57BL/6 J parental Ccnd1 allele in BXD strains and that its differential processing accounts for sensitivity or resistance to 3-NP. Our results indicate that naturally occurring Ccnd1 variants may play a role in the variability observed in neurodegenerative disorders involving mitochondria complex II dysfunction and point to cyclin D1 as a possible therapeutic target.
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Affiliation(s)
- Paula Dietrich
- Department of Physiology, The University of Tennessee, Health Science Center, Memphis, TN 38163, USA,Corresponding authors: ,
| | - Shanta Alli
- Department of Physiology, The University of Tennessee, Health Science Center, Memphis, TN 38163, USA
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee, Health Science Center, Memphis, TN 38163, USA
| | - Rachel Cox
- Department of Physiology, The University of Tennessee, Health Science Center, Memphis, TN 38163, USA,The University of Tennessee, Knoxville, TN 37996, USA
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee, Health Science Center, Memphis, TN 38163, USA
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee, Health Science Center, Memphis, TN 38163, USA
| | - Ioannis Dragatsis
- Department of Physiology, The University of Tennessee, Health Science Center, Memphis, TN 38163, USA,Corresponding authors: ,
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40
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Gu Q, Xu F, Orgil BO, Khuchua Z, Munkhsaikhan U, Johnson JN, Alberson NR, Pierre JF, Black DD, Dong D, Brennan JA, Cathey BM, Efimov IR, Towbin JA, Purevjav E, Lu L. Systems genetics analysis defines importance of TMEM43/ LUMA for cardiac- and metabolic-related pathways. Physiol Genomics 2022; 54:22-35. [PMID: 34766515 PMCID: PMC8721901 DOI: 10.1152/physiolgenomics.00066.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/07/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022] Open
Abstract
Broad cellular functions and diseases including muscular dystrophy, arrhythmogenic right ventricular cardiomyopathy (ARVC5) and cancer are associated with transmembrane protein43 (TMEM43/LUMA). The study aimed to investigate biological roles of TMEM43 through genetic regulation, gene pathways and gene networks, candidate interacting genes, and up- or downstream regulators. Cardiac transcriptomes from 40 strains of recombinant inbred BXD mice and two parental strains representing murine genetic reference population (GRP) were applied for genetic correlation, functional enrichment, and coexpression network analysis using systems genetics approach. The results were validated in a newly created knock-in Tmem43-S358L mutation mouse model (Tmem43S358L) that displayed signs of cardiac dysfunction, resembling ARVC5 phenotype seen in humans. We found high Tmem43 levels among BXDs with broad variability in expression. Expression of Tmem43 highly negatively correlated with heart mass and heart rate among BXDs, whereas levels of Tmem43 highly positively correlated with plasma high-density lipoproteins (HDL). Through finding differentially expressed genes (DEGs) between Tmem43S358L mutant and wild-type (Tmem43WT) lines, 18 pathways (out of 42 found in BXDs GRP) that are involved in ARVC, hypertrophic cardiomyopathy, dilated cardiomyopathy, nonalcoholic fatty liver disease, Alzheimer's disease, Parkinson's disease, and Huntington's disease were verified. We further constructed Tmem43-mediated gene network, in which Ctnna1, Adcy6, Gnas, Ndufs6, and Uqcrc2 were significantly altered in Tmem43S358L mice versus Tmem43WT controls. Our study defined the importance of Tmem43 for cardiac- and metabolism-related pathways, suggesting that cardiovascular disease-relevant risk factors may also increase risk of metabolic and neurodegenerative diseases via TMEM43-mediated pathways.
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Affiliation(s)
- Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
- Department of Cardiology, The Affiliated Hospital of Nantong University, Nantong, China
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Buyan-Ochir Orgil
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Zaza Khuchua
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Biochemistry, Sechenov University, Moscow, Russia
| | - Undral Munkhsaikhan
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Jason N Johnson
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Neely R Alberson
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Joseph F Pierre
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Dennis D Black
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Deli Dong
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Jaclyn A Brennan
- Department of Biomedical Engineering, The George Washington University, Washington, District of Columbia
| | - Brianna M Cathey
- Department of Biomedical Engineering, The George Washington University, Washington, District of Columbia
| | - Igor R Efimov
- Department of Biomedical Engineering, The George Washington University, Washington, District of Columbia
| | - Jeffrey A Towbin
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
- Department of Pediatric Cardiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Enkhsaikhan Purevjav
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
- Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee
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41
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Clark KC, Kwitek AE. Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome. Compr Physiol 2021; 12:3045-3084. [PMID: 34964118 PMCID: PMC9373910 DOI: 10.1002/cphy.c210010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Metabolic syndrome (MetS) is a highly heritable disease and a major public health burden worldwide. MetS diagnosis criteria are met by the simultaneous presence of any three of the following: high triglycerides, low HDL/high LDL cholesterol, insulin resistance, hypertension, and central obesity. These diseases act synergistically in people suffering from MetS and dramatically increase risk of morbidity and mortality due to stroke and cardiovascular disease, as well as certain cancers. Each of these component features is itself a complex disease, as is MetS. As a genetically complex disease, genetic risk factors for MetS are numerous, but not very powerful individually, often requiring specific environmental stressors for the disease to manifest. When taken together, all sequence variants that contribute to MetS disease risk explain only a fraction of the heritable variance, suggesting additional, novel loci have yet to be discovered. In this article, we will give a brief overview on the genetic concepts needed to interpret genome-wide association studies (GWAS) and quantitative trait locus (QTL) data, summarize the state of the field of MetS physiological genomics, and to introduce tools and resources that can be used by the physiologist to integrate genomics into their own research on MetS and any of its component features. There is a wealth of phenotypic and molecular data in animal models and humans that can be leveraged as outlined in this article. Integrating these multi-omic QTL data for complex diseases such as MetS provides a means to unravel the pathways and mechanisms leading to complex disease and promise for novel treatments. © 2022 American Physiological Society. Compr Physiol 12:1-40, 2022.
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Affiliation(s)
- Karen C Clark
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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42
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Trotter C, Kim H, Farage G, Prins P, Williams RW, Broman KW, Sen Ś. Speeding up eQTL scans in the BXD population using GPUs. G3 (BETHESDA, MD.) 2021; 11:jkab254. [PMID: 34499130 PMCID: PMC8664437 DOI: 10.1093/g3journal/jkab254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/27/2021] [Indexed: 11/27/2022]
Abstract
The BXD family of mouse strains are an important reference population for systems biology and genetics that have been fully sequenced and deeply phenotyped. To facilitate interactive use of genotype-phenotype relations using many massive omics data sets for this and other segregating populations, we have developed new algorithms and code that enable near-real-time whole-genome quantitative trait locus (QTL) scans for up to one million traits. By using easily parallelizable operations including matrix multiplication, vectorized operations, and element-wise operations, our method is more than 700 times faster than a R/qtl linear model genome scan using 16 threads. We used parallelization of different CPU threads as well as GPUs. We found that the speed advantage of GPUs is dependent on problem size and shape (the number of cases, number of genotypes, and number of traits). Our approach is ideal for interactive web services, such as GeneNetwork.org that need to display results in real-time. Our implementation is available as the Julia language package LiteQTL at https://github.com/senresearch/LiteQTL.jl.
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Affiliation(s)
- Chelsea Trotter
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Hyeonju Kim
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Gregory Farage
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Śaunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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43
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Xu F, Gao J, Orgil BO, Bajpai AK, Gu Q, Purevjav E, Davenport AS, Li K, Towbin JA, Black DD, Pierre JF, Lu L. Ace2 and Tmprss2 Expressions Are Regulated by Dhx32 and Influence the Gastrointestinal Symptoms Caused by SARS-CoV-2. J Pers Med 2021; 11:1212. [PMID: 34834564 PMCID: PMC8621576 DOI: 10.3390/jpm11111212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
Studies showed that the gastrointestinal (GI) tract is one of the most important pathways for SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19). As SARS-CoV-2 cellular entry depends on the ACE2 receptor and TMPRSS2 priming of the spike protein, it is important to understand the molecular mechanisms through which these two proteins and their cognate transcripts interact and influence the pathogenesis of COVID-19. In this study, we quantified the expression, associations, genetic modulators, and molecular pathways for Tmprss2 and Ace2 mRNA expressions in GI tissues using a systems genetics approach and the expanded family of highly diverse BXD mouse strains. The results showed that both Tmprss2 and Ace2 are highly expressed in GI tissues with significant covariation. We identified a significant expression quantitative trait locus on chromosome 7 that controls the expression of both Tmprss2 and Ace2. Dhx32 was found to be the strongest candidate in this interval. Co-expression network analysis demonstrated that both Tmprss2 and Ace2 were located at the same module that is significantly associated with other GI-related traits. Protein-protein interaction analysis indicated that hub genes in this module are linked to circadian rhythms. Collectively, our data suggested that genes with circadian rhythms of expression may have an impact on COVID-19 disease, with implications related to the timing and treatment of COVID-19.
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Affiliation(s)
- Fuyi Xu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China;
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (J.G.); (A.K.B.); (Q.G.); (A.S.D.)
| | - Jun Gao
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (J.G.); (A.K.B.); (Q.G.); (A.S.D.)
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Buyan-Ochir Orgil
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (B.-O.O.); (E.P.); (J.A.T.); (D.D.B.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital Memphis, Memphis, TN 38103, USA
| | - Akhilesh Kumar Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (J.G.); (A.K.B.); (Q.G.); (A.S.D.)
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (J.G.); (A.K.B.); (Q.G.); (A.S.D.)
| | - Enkhsaikhan Purevjav
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (B.-O.O.); (E.P.); (J.A.T.); (D.D.B.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital Memphis, Memphis, TN 38103, USA
| | - Athena S. Davenport
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (J.G.); (A.K.B.); (Q.G.); (A.S.D.)
| | - Kui Li
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Jeffrey A. Towbin
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (B.-O.O.); (E.P.); (J.A.T.); (D.D.B.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital Memphis, Memphis, TN 38103, USA
- Pediatric Cardiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Dennis D. Black
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (B.-O.O.); (E.P.); (J.A.T.); (D.D.B.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital Memphis, Memphis, TN 38103, USA
| | - Joseph F. Pierre
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (B.-O.O.); (E.P.); (J.A.T.); (D.D.B.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital Memphis, Memphis, TN 38103, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (J.G.); (A.K.B.); (Q.G.); (A.S.D.)
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44
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Goldberg LR, Yao EJ, Kelliher JC, Reed ER, Cox JW, Parks C, Kirkpatrick SL, Beierle JA, Chen MM, Johnson WE, Homanics GE, Williams RW, Bryant CD, Mulligan MK. A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12774. [PMID: 34677900 PMCID: PMC9083095 DOI: 10.1111/gbb.12774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/19/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022]
Abstract
Psychostimulant (methamphetamine, cocaine) use disorders have a genetic component that remains mostly unknown. We conducted genome-wide quantitative trait locus (QTL) analysis of methamphetamine stimulant sensitivity. To facilitate gene identification, we employed a Reduced Complexity Cross between closely related C57BL/6 mouse substrains and examined maximum speed and distance traveled over 30 min following methamphetamine (2 mg/kg, i.p.). For maximum methamphetamine-induced speed following the second and third administration, we identified a single genome-wide significant QTL on chromosome 11 that peaked near the Cyfip2 locus (LOD = 3.5, 4.2; peak = 21 cM [36 Mb]). For methamphetamine-induced distance traveled following the first and second administration, we identified a genome-wide significant QTL on chromosome 5 that peaked near a functional intronic indel in Gabra2 coding for the alpha-2 subunit of the GABA-A receptor (LOD = 3.6-5.2; peak = 34-35 cM [66-67 Mb]). Striatal cis-expression QTL mapping corroborated Gabra2 as a functional candidate gene underlying methamphetamine-induced distance traveled. CRISPR/Cas9-mediated correction of the mutant intronic deletion on the C57BL/6J background to the wild-type C57BL/6NJ allele was sufficient to reduce methamphetamine-induced locomotor activity toward the wild-type C57BL/6NJ-like level, thus validating the quantitative trait variant (QTV). These studies show the power and efficiency of Reduced Complexity Crosses in identifying causal variants underlying complex traits. Functionally restoring Gabra2 expression decreased methamphetamine stimulant sensitivity and supports preclinical and human genetic studies implicating the GABA-A receptor in psychostimulant addiction-relevant traits. Importantly, our findings have major implications for studying psychostimulants in the C57BL/6J strain-the gold standard strain in biomedical research.
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Affiliation(s)
- Lisa R. Goldberg
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
- NIGMS T32 Ph.D. Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Emily J. Yao
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Julia C. Kelliher
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Eric R. Reed
- Ph.D. Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | - Jiayi Wu Cox
- Program in Biomedical Sciences, Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Cory Parks
- Department of Agricultural, Biology, and Health Sciences, Cameron University, Lawton, Oklahoma, USA
| | - Stacey L. Kirkpatrick
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Jacob A. Beierle
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
- NIGMS T32 Ph.D. Training Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Melanie M. Chen
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - William E. Johnson
- Department of Medicine, Computational Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Gregg E. Homanics
- Departments of Anesthesiology, Neurobiology, and Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Camron D. Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston, Massachusetts, USA
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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45
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Inferring multilayer interactome networks shaping phenotypic plasticity and evolution. Nat Commun 2021; 12:5304. [PMID: 34489412 PMCID: PMC8421358 DOI: 10.1038/s41467-021-25086-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Phenotypic plasticity represents a capacity by which the organism changes its phenotypes in response to environmental stimuli. Despite its pivotal role in adaptive evolution, how phenotypic plasticity is genetically controlled remains elusive. Here, we develop a unified framework for coalescing all single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) into a quantitative graph. This framework integrates functional genetic mapping, evolutionary game theory, and predator-prey theory to decompose the net genetic effect of each SNP into its independent and dependent components. The independent effect arises from the intrinsic capacity of a SNP, only expressed when it is in isolation, whereas the dependent effect results from the extrinsic influence of other SNPs. The dependent effect is conceptually beyond the traditional definition of epistasis by not only characterizing the strength of epistasis but also capturing the bi-causality of epistasis and the sign of the causality. We implement functional clustering and variable selection to infer multilayer, sparse, and multiplex interactome networks from any dimension of genetic data. We design and conduct two GWAS experiments using Staphylococcus aureus, aimed to test the genetic mechanisms underlying the phenotypic plasticity of this species to vancomycin exposure and Escherichia coli coexistence. We reconstruct the two most comprehensive genetic networks for abiotic and biotic phenotypic plasticity. Pathway analysis shows that SNP-SNP epistasis for phenotypic plasticity can be annotated to protein-protein interactions through coding genes. Our model can unveil the regulatory mechanisms of significant loci and excavate missing heritability from some insignificant loci. Our multilayer genetic networks provide a systems tool for dissecting environment-induced evolution.
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46
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Thomas MH, Gui Y, Garcia P, Karout M, Gomez Ramos B, Jaeger C, Michelucci A, Gaigneaux A, Kollmus H, Centeno A, Schughart K, Balling R, Mittelbronn M, Nadeau JH, Sauter T, Williams RW, Sinkkonen L, Buttini M. Quantitative trait locus mapping identifies a locus linked to striatal dopamine and points to collagen IV alpha-6 chain as a novel regulator of striatal axonal branching in mice. GENES BRAIN AND BEHAVIOR 2021; 20:e12769. [PMID: 34453370 DOI: 10.1111/gbb.12769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
Dopaminergic neurons (DA neurons) are controlled by multiple factors, many involved in neurological disease. Parkinson's disease motor symptoms are caused by the demise of nigral DA neurons, leading to loss of striatal dopamine (DA). Here, we measured DA concentration in the dorsal striatum of 32 members of Collaborative Cross (CC) family and their eight founder strains. Striatal DA varied greatly in founders, and differences were highly heritable in the inbred CC progeny. We identified a locus, containing 164 genes, linked to DA concentration in the dorsal striatum on chromosome X. We used RNAseq profiling of the ventral midbrain of two founders with substantial difference in striatal DA-C56BL/6 J and A/J-to highlight potential protein-coding candidates modulating this trait. Among the five differentially expressed genes within the locus, we found that the gene coding for the collagen IV alpha 6 chain (Col4a6) was expressed nine times less in A/J than in C57BL/6J. Using single cell RNA-seq data from developing human midbrain, we found that COL4A6 is highly expressed in radial glia-like cells and neuronal progenitors, indicating a role in neuronal development. Collagen IV alpha-6 chain (COL4A6) controls axogenesis in simple model organisms. Consistent with these findings, A/J mice had less striatal axonal branching than C57BL/6J mice. We tentatively conclude that DA concentration and axonal branching in dorsal striatum are modulated by COL4A6, possibly during development. Our study shows that genetic mapping based on an easily measured Central Nervous System (CNS) trait, using the CC population, combined with follow-up observations, can parse heritability of such a trait, and nominate novel functions for commonly expressed proteins.
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Affiliation(s)
- Mélanie H Thomas
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg
| | - Yujuan Gui
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg.,National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
| | - Mona Karout
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg
| | - Borja Gomez Ramos
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jaeger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg
| | - Alessandro Michelucci
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Neuro-Immunology Group, Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Anthoula Gaigneaux
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Arthur Centeno
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,University of Veterinary Medicine Hannover, Hannover, Germany.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg.,Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg.,National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg.,Neuro-Immunology Group, Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, Washington, USA.,Maine Medical Center Research Institute, Scarborough, Maine, USA
| | - Thomas Sauter
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch/Alzette, Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg
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Baud A, Casale FP, Barkley-Levenson AM, Farhadi N, Montillot C, Yalcin B, Nicod J, Palmer AA, Stegle O. Dissecting indirect genetic effects from peers in laboratory mice. Genome Biol 2021; 22:216. [PMID: 34311762 PMCID: PMC8311926 DOI: 10.1186/s13059-021-02415-x] [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: 04/27/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The phenotype of an individual can be affected not only by the individual's own genotypes, known as direct genetic effects (DGE), but also by genotypes of interacting partners, indirect genetic effects (IGE). IGE have been detected using polygenic models in multiple species, including laboratory mice and humans. However, the underlying mechanisms remain largely unknown. Genome-wide association studies of IGE (igeGWAS) can point to IGE genes, but have not yet been applied to non-familial IGE arising from "peers" and affecting biomedical phenotypes. In addition, the extent to which igeGWAS will identify loci not identified by dgeGWAS remains an open question. Finally, findings from igeGWAS have not been confirmed by experimental manipulation. RESULTS We leverage a dataset of 170 behavioral, physiological, and morphological phenotypes measured in 1812 genetically heterogeneous laboratory mice to study IGE arising between same-sex, adult, unrelated mice housed in the same cage. We develop and apply methods for igeGWAS in this context and identify 24 significant IGE loci for 17 phenotypes (FDR < 10%). We observe no overlap between IGE loci and DGE loci for the same phenotype, which is consistent with the moderate genetic correlations between DGE and IGE for the same phenotype estimated using polygenic models. Finally, we fine-map seven significant IGE loci to individual genes and find supportive evidence in an experiment with a knockout model that Epha4 gives rise to IGE on stress-coping strategy and wound healing. CONCLUSIONS Our results demonstrate the potential for igeGWAS to identify IGE genes and shed light into the mechanisms of peer influence.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Current Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Microsoft Research New England, Cambridge, MA USA
| | | | - Nilgoun Farhadi
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
| | - Charlotte Montillot
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Binnaz Yalcin
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Jerome Nicod
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Current Address: The Francis Crick Institute, London, UK
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, 69120 Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
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48
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Parks C, Rogers CM, Prins P, Williams RW, Chen H, Jones BC, Moore BM, Mulligan MK. Genetic Modulation of Initial Sensitivity to Δ9-Tetrahydrocannabinol (THC) Among the BXD Family of Mice. Front Genet 2021; 12:659012. [PMID: 34367237 PMCID: PMC8343140 DOI: 10.3389/fgene.2021.659012] [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: 01/26/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022] Open
Abstract
Cannabinoid receptor 1 activation by the major psychoactive component in cannabis, Δ9-tetrahydrocannabinol (THC), produces motor impairments, hypothermia, and analgesia upon acute exposure. In previous work, we demonstrated significant sex and strain differences in acute responses to THC following administration of a single dose (10 mg/kg, i.p.) in C57BL/6J (B6) and DBA/2J (D2) inbred mice. To determine the extent to which these differences are heritable, we quantified acute responses to a single dose of THC (10 mg/kg, i.p.) in males and females from 20 members of the BXD family of inbred strains derived by crossing and inbreeding B6 and D2 mice. Acute THC responses (initial sensitivity) were quantified as changes from baseline for: 1. spontaneous activity in the open field (mobility), 2. body temperature (hypothermia), and 3. tail withdrawal latency to a thermal stimulus (antinociception). Initial sensitivity to the immobilizing, hypothermic, and antinociceptive effects of THC varied substantially across the BXD family. Heritability was highest for mobility and hypothermia traits, indicating that segregating genetic variants modulate initial sensitivity to THC. We identified genomic loci and candidate genes, including Ndufs2, Scp2, Rps6kb1 or P70S6K, Pde4d, and Pten, that may control variation in THC initial sensitivity. We also detected strong correlations between initial responses to THC and legacy phenotypes related to intake or response to other drugs of abuse (cocaine, ethanol, and morphine). Our study demonstrates the feasibility of mapping genes and variants modulating THC responses in the BXDs to systematically define biological processes and liabilities associated with drug use and abuse.
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Affiliation(s)
- Cory Parks
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Agriculture, Biology and Health Sciences, Cameron University, Lawton, OK, United States
| | - Chris M. Rogers
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Byron C. Jones
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Bob M. Moore
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
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49
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Molendijk J, Seldin MM, Parker BL. CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data. Nucleic Acids Res 2021; 49:W104-W113. [PMID: 33978718 PMCID: PMC8262721 DOI: 10.1093/nar/gkab352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023] Open
Abstract
The integration of genomics, transcriptomics, proteomics and phenotypic traits across genetically diverse populations is a powerful approach to discover novel biological regulators. The increasing volume of complex data require new and easy-to-use tools accessible to a variety of scientists for the discovery and visualization of functionally relevant associations. To meet this requirement, we developed CoffeeProt, an open-source tool that analyses genetic variants associated to protein networks, other omics datatypes and phenotypic traits. CoffeeProt uses transcriptomics or proteomics data to perform correlation network analyses and annotates results with protein-protein interactions, subcellular localisations and drug associations. It then integrates genetic variants associated with gene expression (eQTLs) or protein abundance (pQTLs) and includes predictions of the potential consequences of variants on gene function. Finally, genetic variants are co-mapped to molecular or phenotypic traits either provided by the user or retrieved directly from publicly available GWAS results. We demonstrate its utility with the analysis of mouse and human population data enabling the rapid identification of genetic variants associated with druggable proteins and clinical traits. We expect that CoffeeProt will serve the systems genetics and basic science research communities, leading to the discovery of novel biologically relevant associations. CoffeeProt is available at www.coffeeprot.com.
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Affiliation(s)
- Jeffrey Molendijk
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, CA 92697, USA
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC 3010, Australia
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50
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Vitiello D, Dakhovnik A, Statzer C, Ewald CY. Lifespan-Associated Gene Expression Signatures of Recombinant BXD Mice Implicates Coro7 and Set in Longevity. Front Genet 2021; 12:694033. [PMID: 34306034 PMCID: PMC8299419 DOI: 10.3389/fgene.2021.694033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Although genetic approaches have identified key genes and pathways that promote longevity, systems-level approaches are less utilized. Here, we took advantage of the wealth of omics data characterizing the BXD family of mice. We associated transcript and peptide levels across five tissues from both female and male BXD isogenic lines with their median lifespan. We identified over 5000 genes that showed a longevity correlation in a given tissue. Surprisingly, we found less than 1% overlap among longevity-correlating genes across tissues and sex. These 1% shared genes consist of 51 genes, of which 13 have been shown to alter lifespan. Only two genes -Coro7 and Set- showed a longevity correlation in all tissues and in both sexes. While differential regulation of aging across tissues and sex has been reported, our systems-level analysis reveals two unique genes that may promote healthy aging in unique sex- and tissue-agnostic manner.
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Affiliation(s)
| | | | | | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zürich, Schwerzenbach, Switzerland
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