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Vetr NG, Gay NR, Montgomery SB. The impact of exercise on gene regulation in association with complex trait genetics. Nat Commun 2024; 15:3346. [PMID: 38693125 PMCID: PMC11063075 DOI: 10.1038/s41467-024-45966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/01/2024] [Indexed: 05/03/2024] Open
Abstract
Endurance exercise training is known to reduce risk for a range of complex diseases. However, the molecular basis of this effect has been challenging to study and largely restricted to analyses of either few or easily biopsied tissues. Extensive transcriptome data collected across 15 tissues during exercise training in rats as part of the Molecular Transducers of Physical Activity Consortium has provided a unique opportunity to clarify how exercise can affect tissue-specific gene expression and further suggest how exercise adaptation may impact complex disease-associated genes. To build this map, we integrate this multi-tissue atlas of gene expression changes with gene-disease targets, genetic regulation of expression, and trait relationship data in humans. Consensus from multiple approaches prioritizes specific tissues and genes where endurance exercise impacts disease-relevant gene expression. Specifically, we identify a total of 5523 trait-tissue-gene triplets to serve as a valuable starting point for future investigations [Exercise; Transcription; Human Phenotypic Variation].
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2
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024:10.1038/s41576-024-00711-3. [PMID: 38565962 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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3
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Batista S, Madar VS, Freda PJ, Bhandary P, Ghosh A, Matsumoto N, Chitre AS, Palmer AA, Moore JH. Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis. BioData Min 2024; 17:7. [PMID: 38419006 PMCID: PMC10900690 DOI: 10.1186/s13040-024-00358-0] [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: 10/06/2023] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE Epistasis, the interaction between two or more genes, is integral to the study of genetics and is present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects, partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Furthermore, existing methods for epistasis detection only consider a Cartesian (multiplicative) model for interaction terms. This is likely limiting as epistatic interactions can evolve to produce varied relationships between genetic loci, some complex and not linearly separable. METHODS We present new algorithms for the interaction coefficients for standard regression models for epistasis that permit many varied models for the interaction terms for loci and efficient memory usage. The algorithms are given for two-way and three-way epistasis and may be generalized to higher order epistasis. Statistical tests for the interaction coefficients are also provided. We also present an efficient matrix based algorithm for permutation testing for two-way epistasis. We offer a proof and experimental evidence that methods that look for epistasis only at loci that have main effects may not be justified. Given the computational efficiency of the algorithm, we applied the method to a rat data set and mouse data set, with at least 10,000 loci and 1,000 samples each, using the standard Cartesian model and the XOR model to explore body mass index. RESULTS This study reveals that although many of the loci found to exhibit significant statistical epistasis overlap between models in rats, the pairs are mostly distinct. Further, the XOR model found greater evidence for statistical epistasis in many more pairs of loci in both data sets with almost all significant epistasis in mice identified using XOR. In the rat data set, loci involved in epistasis under the XOR model are enriched for biologically relevant pathways. CONCLUSION Our results in both species show that many biologically relevant epistatic relationships would have been undetected if only one interaction model was applied, providing evidence that varied interaction models should be implemented to explore epistatic interactions that occur in living systems.
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Affiliation(s)
- Sandra Batista
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA.
| | | | - Philip J Freda
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Priyanka Bhandary
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Attri Ghosh
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Nicholas Matsumoto
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
- Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Dr., Mailcode: 0667, La Jolla, CA, 92093-0667, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, 700 N San Vicente Blvd., Pacific Design Center, Guite G540, West Hollywood, CA, 90069, USA.
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Huang S, Liu S, Huang M, He JR, Wang C, Wang T, Feng X, Kuang Y, Lu J, Gu Y, Xia X, Lin S, Zhou W, Fu Q, Xia H, Qiu X. The Born in Guangzhou Cohort Study enables generational genetic discoveries. Nature 2024; 626:565-573. [PMID: 38297123 DOI: 10.1038/s41586-023-06988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
Genomic research that targets large-scale, prospective birth cohorts constitutes an essential strategy for understanding the influence of genetics and environment on human health1. Nonetheless, such studies remain scarce, particularly in Asia. Here we present the phase I genome study of the Born in Guangzhou Cohort Study2 (BIGCS), which encompasses the sequencing and analysis of 4,053 Chinese individuals, primarily composed of trios or mother-infant duos residing in South China. Our analysis reveals novel genetic variants, a high-quality reference panel, and fine-scale local genetic structure within BIGCS. Notably, we identify previously unreported East Asian-specific genetic associations with maternal total bile acid, gestational weight gain and infant cord blood traits. Additionally, we observe prevalent age-specific genetic effects on lipid levels in mothers and infants. In an exploratory intergenerational Mendelian randomization analysis, we estimate the maternal putatively causal and fetal genetic effects of seven adult phenotypes on seven fetal growth-related measurements. These findings illuminate the genetic links between maternal and early-life traits in an East Asian population and lay the groundwork for future research into the intricate interplay of genetics, intrauterine exposures and early-life experiences in shaping long-term health.
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Affiliation(s)
- Shujia Huang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Siyang Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Mingxi Huang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jian-Rong He
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Provincial Clinical Research Center for Child Health, Guangzhou, China
- Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chengrui Wang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yashu Kuang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Jinhua Lu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Yuqin Gu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xiaoyan Xia
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Department of Women's Health, Provincial Key Clinical Specialty of Woman and Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shanshan Lin
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Department of Women's Health, Provincial Key Clinical Specialty of Woman and Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wenhao Zhou
- Division of Neonatology and Center for Newborn Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Huimin Xia
- Provincial Clinical Research Center for Child Health, Guangzhou, China.
- Provincial Key Laboratory of Research in Structure Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
- Provincial Clinical Research Center for Child Health, Guangzhou, China.
- Department of Women's Health, Provincial Key Clinical Specialty of Woman and Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
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Lim KS, Cheng J, Tuggle C, Dyck M, Canada P, Fortin F, Harding J, Plastow G, Dekkers J. Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience. Genet Sel Evol 2023; 55:90. [PMID: 38087235 PMCID: PMC10714454 DOI: 10.1186/s12711-023-00860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Disease resilience is the ability of an animal to maintain productive performance under disease conditions and is an important selection target. In pig breeding programs, disease resilience must be evaluated on selection candidates without exposing them to disease. To identify potential genetic indicators for disease resilience that can be measured on selection candidates, we focused on the blood transcriptome of 1594 young healthy pigs with subsequent records on disease resilience. Transcriptome data were obtained by 3'mRNA sequencing and genotype data were from a 650 K genotyping array. RESULTS Heritabilities of the expression of 16,545 genes were estimated, of which 5665 genes showed significant estimates of heritability (p < 0.05), ranging from 0.05 to 0.90, with or without accounting for white blood cell composition. Genes with heritable expression levels were spread across chromosomes, but were enriched in the swine leukocyte antigen region (average estimate > 0.2). The correlation of heritability estimates with the corresponding estimates obtained for genes expressed in human blood was weak but a sizable number of genes with heritable expression levels overlapped. Genes with heritable expression levels were significantly enriched for biological processes such as cell activation, immune system process, stress response, and leukocyte activation, and were involved in various disease annotations such as RNA virus infection, including SARS-Cov2, as well as liver disease, and inflammation. To estimate genetic correlations with disease resilience, 3205 genotyped pigs, including the 1594 pigs with transcriptome data, were evaluated for disease resilience following their exposure to a natural polymicrobial disease challenge. Significant genetic correlations (p < 0.05) were observed with all resilience phenotypes, although few exceeded expected false discovery rates. Enrichment analysis of genes ranked by estimates of genetic correlations with resilience phenotypes revealed significance for biological processes such as regulation of cytokines, including interleukins and interferons, and chaperone mediated protein folding. CONCLUSIONS These results suggest that expression levels in the blood of young healthy pigs for genes in biological pathways related to immunity and endoplasmic reticulum stress have potential to be used as genetic indicator traits to select for disease resilience.
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Affiliation(s)
- Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA, USA
- Department of Animal Resource Science, Kongju National University, Yesan, Chungnam, Republic of Korea
| | - Jian Cheng
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Michael Dyck
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - PigGen Canada
- PigGen Canada Research Consortium, Guelph, ON, Canada
| | - Frederic Fortin
- Centre de Développement du Porc du Québec Inc. (CDPQ), Québec City, QC, Canada
| | - John Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jack Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, USA.
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Fernandez ME, Martinez-Romero J, Aon MA, Bernier M, Price NL, de Cabo R. How is Big Data reshaping preclinical aging research? Lab Anim (NY) 2023; 52:289-314. [PMID: 38017182 DOI: 10.1038/s41684-023-01286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/10/2023] [Indexed: 11/30/2023]
Abstract
The exponential scientific and technological progress during the past 30 years has favored the comprehensive characterization of aging processes with their multivariate nature, leading to the advent of Big Data in preclinical aging research. Spanning from molecular omics to organism-level deep phenotyping, Big Data demands large computational resources for storage and analysis, as well as new analytical tools and conceptual frameworks to gain novel insights leading to discovery. Systems biology has emerged as a paradigm that utilizes Big Data to gain insightful information enabling a better understanding of living organisms, visualized as multilayered networks of interacting molecules, cells, tissues and organs at different spatiotemporal scales. In this framework, where aging, health and disease represent emergent states from an evolving dynamic complex system, context given by, for example, strain, sex and feeding times, becomes paramount for defining the biological trajectory of an organism. Using bioinformatics and artificial intelligence, the systems biology approach is leading to remarkable advances in our understanding of the underlying mechanism of aging biology and assisting in creative experimental study designs in animal models. Future in-depth knowledge acquisition will depend on the ability to fully integrate information from different spatiotemporal scales in organisms, which will probably require the adoption of theories and methods from the field of complex systems. Here we review state-of-the-art approaches in preclinical research, with a focus on rodent models, that are leading to conceptual and/or technical advances in leveraging Big Data to understand basic aging biology and its full translational potential.
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Affiliation(s)
- Maria Emilia Fernandez
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jorge Martinez-Romero
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Miguel A Aon
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Laboratory of Cardiovascular Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Michel Bernier
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Nathan L Price
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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Hu Y, Xie D, Li X, Han W, Chen Y, Qi H, Wang P. Omic horizon expression: a database of gene expression based on RNA sequencing data. BMC Genomics 2023; 24:674. [PMID: 37940882 PMCID: PMC10634139 DOI: 10.1186/s12864-023-09781-9] [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] [Received: 04/06/2023] [Accepted: 11/02/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Gene expression profiles have important significance for gene expression characteristics and further functional studies. More attention has been given to the expression databases in humans and mice, but less attention has been given to rats, while rat models also play an irreplaceable role in biomedical experiments. RESULTS To depict the rat gene expression profiles in mRNA expression levels, we analyzed over 2,700 RNA sequencing (RNA-Seq) samples from 48 tissues, 40 primary cell types and 25 cell lines; and then mapped them to the latest version of the rat genome reference, mRatBN7.2. Based on these datasets and reanalysis, we constructed a new database, the Omic Horizon Expression Database ( http://immudb.bjmu.edu.cn/expression.html ), which allows expressional profile query of over 25,000 rat genes based on non-redundant gene symbols. The database supports requests using gene symbols (or alias), Ensemble and Entrez gene IDs. Gene expression profiles can be queried in three categories: tissues, primary cells and cell lines. Application examples including expression profiling and comparison, as well as identification of novel rat genes, were illustrated to show the utility of the database. CONCLUSIONS As an omic resource, the Omic Horizon Expression Database provides horizons of gene expression profiles across various tissues and cells, which greatly facilitates the identification of rat genes as well as functional clues.
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Affiliation(s)
- Yuzhe Hu
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China
- Peking University Center for Human Disease Genomics, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Dong Xie
- School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Xixi Li
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China
- Peking University Center for Human Disease Genomics, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Wenling Han
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China
- Peking University Center for Human Disease Genomics, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Yingyu Chen
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China
- Peking University Center for Human Disease Genomics, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Huiying Qi
- Department of Health informatics and Management, School of Health Humanities, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China.
| | - Pingzhang Wang
- Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China.
- Peking University Center for Human Disease Genomics, No. 38 Xueyuan Road, Beijing, 100191, China.
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Heishima K, Sugito N, Abe C, Hirata A, Sakai H, Akao Y. Targeting microRNA-145-mediated progressive phenotypes of early bladder cancer in a molecularly defined in vivo model. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:960-982. [PMID: 37727442 PMCID: PMC10505924 DOI: 10.1016/j.omtn.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/09/2023] [Indexed: 09/21/2023]
Abstract
A progressive subclass of early-stage non-muscle-invasive bladder cancer (NMIBC) frequently recurs and progress into invasive carcinoma, thus decreasing the overall survival rate of NMIBC. However, therapeutic development for progressive NMIBC has been challenging due to the lack of molecularly validated in vivo models and agents targeting its genetic vulnerability. We herein molecularly characterized an interventional model of progressive NMIBC and revealed the principal functions and therapeutic potential of microRNA-145 (miR-145) in early bladder tumorigenesis. N-butyl-N-(4-hydroxybutyl)nitrosamine-induced premalignant lesions (BiPLs) in rats exhibited downregulated expression of miR-145 as well as highly similar mutation/expression profiles to those of the human progressive NMIBC subclass with the worst prognosis. The expression patterns of miR-145 inversely correlated with those of BC-related oncogenes in BiPLs. We also demonstrated that miR-145 dominantly regulated interferon pathways and c-Myc expression, which play a crucial role in the pathogenesis of progressive NMIBC. Furthermore, we demonstrated that miR-145 replacement with a novel miR-145-based intravesical agent (miR-145S1) significantly inhibited the progression of BiPLs in vivo. These results provide insights into the essential role of miR-145 as the earliest-acting oncogenic driver of bladder tumorigenesis as well as a validated interventional model and novel miR-145-based nucleic acid therapeutic agent for progressive NMIBC.
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Affiliation(s)
- Kazuki Heishima
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu, Japan
- Institute for Advanced Study (GUiAS), Gifu University, Gifu, Gifu, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan
| | - Nobuhiko Sugito
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu, Japan
| | - Chikara Abe
- Department of Physiology, Gifu University Graduate School of Medicine, Gifu, Gifu, Japan
| | - Akihiro Hirata
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Hiroki Sakai
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Gifu, Japan
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Yukihiro Akao
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu, Japan
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9
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Kaldunski ML, Smith JR, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj MA, Tutaj M, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Rare disease research resources at the Rat Genome Database. Genetics 2023; 224:iyad078. [PMID: 37119810 PMCID: PMC10411567 DOI: 10.1093/genetics/iyad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Rare diseases individually affect relatively few people, but as a group they impact considerable numbers of people. The Rat Genome Database (https://rgd.mcw.edu) is a knowledgebase that offers resources for rare disease research. This includes disease definitions, genes, quantitative trail loci (QTLs), genetic variants, annotations to published literature, links to external resources, and more. One important resource is identifying relevant cell lines and rat strains that serve as models for disease research. Diseases, genes, and strains have report pages with consolidated data, and links to analysis tools. Utilizing these globally accessible resources for rare disease research, potentiating discovery of mechanisms and new treatments, can point researchers toward solutions to alleviate the suffering of those afflicted with these diseases.
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Affiliation(s)
- Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Joint Department of Biomedical Engineering, Marquette University & Medical College of Wisconsin, Milwaukee, WI 53226, USA
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10
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Laulederkind SJF, Hayman GT, Wang SJ, Kaldunski ML, Vedi M, Demos WM, Tutaj M, Smith JR, Lamers L, Gibson AC, Thorat K, Thota J, Tutaj MA, De Pons JL, Dwinell MR, Kwitek AE. The Rat Genome Database: Genetic, Genomic, and Phenotypic Data Across Multiple Species. Curr Protoc 2023; 3:e804. [PMID: 37347557 PMCID: PMC10335880 DOI: 10.1002/cpz1.804] [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] [Indexed: 06/24/2023]
Abstract
The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, https://rgd.mcw.edu) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes, cellular components, and chemical interactions for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat and other species. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Navigating the Rat Genome Database (RGD) home page Basic Protocol 2: Using the RGD search functions Basic Protocol 3: Searching for quantitative trait loci Basic Protocol 4: Using the RGD genome browser (JBrowse) to find phenotypic annotations Basic Protocol 5: Using OntoMate to find gene-disease data Basic Protocol 6: Using MOET to find gene-ontology enrichment Basic Protocol 7: Using OLGA to generate gene lists for analysis Basic Protocol 8: Using the GA tool to analyze ontology annotations for genes Basic Protocol 9: Using the RGD InterViewer tool to find protein interaction data Basic Protocol 10: Using the RGD Variant Visualizer tool to find genetic variant data Basic Protocol 11: Using the RGD Disease Portals to find disease, phenotype, and other information Basic Protocol 12: Using the RGD Phenotypes & Models Portal to find qualitative and quantitative phenotype data and other rat strain-related information Basic Protocol 13: Using the RGD Pathway Portal to find disease and phenotype data via molecular pathways.
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Affiliation(s)
| | - G. Thomas Hayman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Shur-Jen Wang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary L. Kaldunski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mahima Vedi
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Wendy M. Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jennifer R. Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Logan Lamers
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Adam C. Gibson
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ketaki Thorat
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jyothi Thota
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Marek A. Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jeffrey L. De Pons
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Melinda R. Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Anne E. Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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11
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Jones TEM, Yates B, Braschi B, Gray K, Tweedie S, Seal RL, Bruford EA. The VGNC: expanding standardized vertebrate gene nomenclature. Genome Biol 2023; 24:115. [PMID: 37173739 PMCID: PMC10176861 DOI: 10.1186/s13059-023-02957-2] [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: 08/10/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 as a sister project to the HUGO Gene Nomenclature Committee, to approve gene nomenclature in vertebrate species without an existing dedicated nomenclature committee. The VGNC aims to harmonize gene nomenclature across selected vertebrate species in line with human gene nomenclature, with orthologs assigned the same nomenclature where possible. This article presents an overview of the VGNC project and discussion of key findings resulting from this work to date. VGNC-approved nomenclature is accessible at https://vertebrate.genenames.org and is additionally displayed by the NCBI, Ensembl, and UniProt databases.
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Affiliation(s)
- Tamsin E. M. Jones
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridgeshire UK
| | - Bethan Yates
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridgeshire UK
- Current address: Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA Cambridgeshire UK
| | - Bryony Braschi
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridgeshire UK
| | - Kristian Gray
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridgeshire UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW Cambridgeshire UK
| | - Susan Tweedie
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridgeshire UK
| | - Ruth L. Seal
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridgeshire UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW Cambridgeshire UK
| | - Elspeth A. Bruford
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridgeshire UK
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW Cambridgeshire UK
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12
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Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M. The Gene Ontology knowledgebase in 2023. Genetics 2023; 224:iyad031. [PMID: 36866529 PMCID: PMC10158837 DOI: 10.1093/genetics/iyad031] [Citation(s) in RCA: 281] [Impact Index Per Article: 281.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 03/04/2023] Open
Abstract
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
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13
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Vedi M, Smith JR, Thomas Hayman G, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. 2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource. Genetics 2023; 224:iyad042. [PMID: 36930729 PMCID: PMC10474928 DOI: 10.1093/genetics/iyad042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
The Rat Genome Database (RGD, https://rgd.mcw.edu) has evolved from simply a resource for rat genetic markers, maps, and genes, by adding multiple genomic data types and extensive disease and phenotype annotations and developing tools to effectively mine, analyze, and visualize the available data, to empower investigators in their hypothesis-driven research. Leveraging its robust and flexible infrastructure, RGD has added data for human and eight other model organisms (mouse, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) besides rat to enhance its translational aspect. This article presents an overview of the database with the most recent additions to RGD's genome, variant, and quantitative phenotype data. We also briefly introduce Virtual Comparative Map (VCMap), an updated tool that explores synteny between species as an improvement to RGD's suite of tools, followed by a discussion regarding the refinements to the existing PhenoMiner tool that assists researchers in finding and comparing quantitative data across rat strains. Collectively, RGD focuses on providing a continuously improving, consistent, and high-quality data resource for researchers while advancing data reproducibility and fulfilling Findable, Accessible, Interoperable, and Reusable (FAIR) data principles.
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Affiliation(s)
- Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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14
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Beach T, Bakke J, Riccio E, Javitz HS, Nishita D, Kapur S, Bunin DI, Chang PY. The progression of radiation injury in a Wistar rat model of partial body irradiation with ∼5% bone marrow shielding. Int J Radiat Biol 2023:1-16. [PMID: 36930794 DOI: 10.1080/09553002.2023.2188937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
PURPOSE To describe the dose response relationship and natural history of radiation injury in the Wistar rat and it's suitability for use in medical countermeasures (MCM) testing. MATERIALS & METHODS In two separate studies, male and female rats were exposed to partial body irradiation (PBI) with 5% bone marrow sparing. Animals were X-ray irradiated from 7 to 12 Gy at 7-10 weeks of age. Acute radiation syndrome (ARS) survival at 30 days and delayed effects of acute radiation exposure (DEARE) survival at 182 days were assessed. Radiation effects were determined by clinical observations, body weights, hematology, clinical chemistry, magnetic resonance imaging of lung, whole-body plethysmography, and histopathology. RESULTS Rats developed canonical ARS responses of hematopoietic atrophy and gastrointestinal injury resulting in mortality at doses ≥8Gy in males and ≥8.5 Gy in females. DEARE mortality occurred at doses ≥8Gy for both sexes. Findings indicate lung, kidney, and/or liver injury, and persistent hematological dysregulation, revealing multi-organ injury as a DEARE. CONCLUSION The Wistar rat PBI model is suitable for testing MCMs against hematopoietic and gastrointestinal ARS. DEARE multi-organ injury occurred in both sexes irradiated with 8-9Gy, also suggesting suitability for polypharmacy studies addressing the combination of ARS and DEARE injury.
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Affiliation(s)
| | | | - Ed Riccio
- SRI International, Menlo Park, CA, USA
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15
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Identifying multiscale translational safety biomarkers using a network-based systems approach. iScience 2023; 26:106094. [PMID: 36895646 PMCID: PMC9988559 DOI: 10.1016/j.isci.2023.106094] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/30/2022] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Animal testing is the current standard for drug and chemicals safety assessment, but hazards translation to human is uncertain. Human in vitro models can address the species translation but might not replicate in vivo complexity. Herein, we propose a network-based method addressing these translational multiscale problems that derives in vivo liver injury biomarkers applicable to in vitro human early safety screening. We applied weighted correlation network analysis (WGCNA) to a large rat liver transcriptomic dataset to obtain co-regulated gene clusters (modules). We identified modules statistically associated with liver pathologies, including a module enriched for ATF4-regulated genes as associated with the occurrence of hepatocellular single-cell necrosis, and as preserved in human liver in vitro models. Within the module, we identified TRIB3 and MTHFD2 as a novel candidate stress biomarkers, and developed and used BAC-eGFPHepG2 reporters in a compound screening, identifying compounds showing ATF4-dependent stress response and potential early safety signals.
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16
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Richard Albert J, Kobayashi T, Inoue A, Monteagudo-Sánchez A, Kumamoto S, Takashima T, Miura A, Oikawa M, Miura F, Takada S, Hirabayashi M, Korthauer K, Kurimoto K, Greenberg MVC, Lorincz M, Kobayashi H. Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biol 2023; 24:48. [PMID: 36918927 PMCID: PMC10012579 DOI: 10.1186/s13059-023-02869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/09/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.
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Affiliation(s)
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Azusa Inoue
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Soichiro Kumamoto
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Asuka Miura
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan
| | - Keegan Korthauer
- Department of Statistics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan
| | | | - Matthew Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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17
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Lu J, Zhu Y, Parkington HC, Hussein M, Zhao J, Bergen P, Rudd D, Deane MA, Oberrauch S, Cornthwaite-Duncan L, Allobawi R, Sharma R, Rao G, Li J, Velkov T. Transcriptomic Mapping of Neurotoxicity Pathways in the Rat Brain in Response to Intraventricular Polymyxin B. Mol Neurobiol 2023; 60:1317-1330. [PMID: 36443617 DOI: 10.1007/s12035-022-03140-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022]
Abstract
Intraventricular or intrathecal administration of polymyxins are increasingly used to treat multidrug-resistant (MDR) Gram-negative bacteria caused infections in the central nervous system (CNS). However, our limited knowledge of the mechanisms underpinning polymyxin-induced neurotoxicity significantly hinders the development of safe and efficacious polymyxin dosing regimens. To this end, we conducted transcriptomic analyses of the rat brain and spinal cord 1 h following intracerebroventricular administration of polymyxin B into rat lateral ventricle at a clinically relevant dose (0.5 mg/kg). Following the treatment, 66 differentially expressed genes (DEGs) were identified in the brain transcriptome while none for the spinal cord (FDR ≤ 0.05, fold-change ≥ 1.5). DEGs were enriched in signaling pathways associated with hormones and neurotransmitters, including dopamine and (nor)epinephrine. Notably, the expression levels of Slc6a3 and Gabra6 were decreased by 20-fold and 4.3-fold, respectively, likely resulting in major perturbations of dopamine and γ-aminobutyric acid signaling in the brain. Mass spectrometry imaging of brain sections revealed a distinct pattern of polymyxin B distribution with the majority accumulating in the injection-side lateral ventricle and subsequently into third and fourth ventricles. Polymyxin B was not detectable in the left lateral ventricle or brain tissue. Electrophysiological measurements on primary cultured rat neurons revealed a large inward current and significant membrane leakage following polymyxin B treatment. Our work demonstrates, for the first time, the key CNS signaling pathways associated with polymyxin neurotoxicity. This mechanistic insight combined with pharmacokinetic/pharmacodynamic dosing strategies will help guide the design of safe and effective intraventricular/intrathecal polymyxin treatment regimens for CNS infections caused by MDR Gram-negative pathogens.
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Affiliation(s)
- Jing Lu
- Department of Pharmacology & Biochemistry, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Yan Zhu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Helena C Parkington
- Department of Physiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Maytham Hussein
- Department of Pharmacology & Biochemistry, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Jinxin Zhao
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Phillip Bergen
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - David Rudd
- Drug Delivery, Disposition and Dynamics, Faculty of Pharmacy and Pharmaceutical Sciences, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3010, Australia
| | - Mary A Deane
- Department of Physiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Sara Oberrauch
- Department of Pharmacology & Biochemistry, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Linda Cornthwaite-Duncan
- Department of Pharmacology & Biochemistry, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Rafah Allobawi
- Department of Pharmacology & Biochemistry, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Rajnikant Sharma
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Gauri Rao
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27514, USA.
| | - Jian Li
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
| | - Tony Velkov
- Department of Pharmacology & Biochemistry, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
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18
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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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19
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Reznik DL, Yang MV, Albelda de la Haza P, Jain A, Spanjaard M, Theiss S, Schaaf CP, Malovannaya A, Strong TV, Veeraragavan S, Samaco RC. Magel2 truncation alters select behavioral and physiological outcomes in a rat model of Schaaf-Yang syndrome. Dis Model Mech 2023; 16:286598. [PMID: 36637363 PMCID: PMC9922728 DOI: 10.1242/dmm.049829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
Previous studies in mice have utilized Magel2 gene deletion models to examine the consequences of its absence. We report the generation, molecular validation and phenotypic characterization of a novel rat model with a truncating Magel2 mutation modeling variants associated with Schaaf-Yang syndrome-causing mutations. Within the hypothalamus, a brain region in which human MAGEL2 is paternally expressed, we demonstrated, at the level of transcript and peptide detection, that rat Magel2 exhibits a paternal, parent-of-origin effect. In evaluations of behavioral features across several domains, juvenile Magel2 mutant rats displayed alterations in anxiety-like behavior and sociability measures. Moreover, the analysis of peripheral organ systems detected alterations in body composition, cardiac structure and function, and breathing irregularities in Magel2 mutant rats. Several of these findings are concordant with reported mouse phenotypes, indicating the conservation of MAGEL2 function across rodent species. Our comprehensive analysis revealing impairments across multiple domains demonstrates the tractability of this model system for the study of truncating MAGEL2 mutations.
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Affiliation(s)
- Derek L Reznik
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Mingxiao V Yang
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Pedro Albelda de la Haza
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Antrix Jain
- Baylor College of Medicine, Mass Spectrometry Proteomics Core, Houston, TX 77030, USA
| | - Melanie Spanjaard
- Heidelberg University, Institute of Human Genetics, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Susanne Theiss
- Heidelberg University, Institute of Human Genetics, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Christian P Schaaf
- Heidelberg University, Institute of Human Genetics, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany
| | - Anna Malovannaya
- Baylor College of Medicine, Mass Spectrometry Proteomics Core, Houston, TX 77030, USA.,Baylor College of Medicine, Verna and Marrs McLean Departments of Biochemistry and Molecular Biology, and Molecular and Cellular Biology, Houston, TX 77030, USA.,Baylor College of Medicine, Dan L. Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
| | - Theresa V Strong
- Foundation for Prader-Willi Research, Walnut, CA 91789, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Surabi Veeraragavan
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Rodney C Samaco
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA.,Texas Children's Hospital, Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
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20
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Hillis DA, Garland T. Multiple solutions at the genomic level in response to selective breeding for high locomotor activity. Genetics 2023; 223:iyac165. [PMID: 36305689 PMCID: PMC9836024 DOI: 10.1093/genetics/iyac165] [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: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 01/19/2023] Open
Abstract
Replicate lines under uniform selection often evolve in different ways. Previously, analyses using whole-genome sequence data for individual mice (Mus musculus) from 4 replicate High Runner lines and 4 nonselected control lines demonstrated genomic regions that have responded consistently to selection for voluntary wheel-running behavior. Here, we ask whether the High Runner lines have evolved differently from each other, even though they reached selection limits at similar levels. We focus on 1 High Runner line (HR3) that became fixed for a mutation at a gene of major effect (Myh4Minimsc) that, in the homozygous condition, causes a 50% reduction in hindlimb muscle mass and many pleiotropic effects. We excluded HR3 from SNP analyses and identified 19 regions not consistently identified in analyses with all 4 lines. Repeating analyses while dropping each of the other High Runner lines identified 12, 8, and 6 such regions. (Of these 45 regions, 37 were unique.) These results suggest that each High Runner line indeed responded to selection somewhat uniquely, but also that HR3 is the most distinct. We then applied 2 additional analytical approaches when dropping HR3 only (based on haplotypes and nonstatistical tests involving fixation patterns). All 3 approaches identified 7 new regions (as compared with analyses using all 4 High Runner lines) that include genes associated with activity levels, dopamine signaling, hippocampus morphology, heart size, and body size, all of which differ between High Runner and control lines. Our results illustrate how multiple solutions and "private" alleles can obscure general signatures of selection involving "public" alleles.
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Affiliation(s)
- David A Hillis
- Genetics, Genomics, and Bioinformatics Graduate Program, University of California, Riverside, CA 92521, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
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21
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Kuramoto T. Positional cloning of rat mutant genes reveals new functions of these genes. Exp Anim 2023; 72:1-8. [PMID: 36058846 PMCID: PMC9978133 DOI: 10.1538/expanim.22-0089] [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] [Indexed: 11/04/2022] Open
Abstract
The laboratory rat (Rattus norvegicus) is a key model organism for biomedical research. Rats can be subjected to strict genetic and environmental controls. The rat's large body size is suitable for both surgical operations and repeated measurements of physiological parameters. These advantages have led to the development of numerous rat models for genetic diseases. Forward genetics is a proven approach for identifying the causative genes of these disease models but requires genome resources including genetic markers and genome sequences. Over the last few decades, rat genome resources have been developed and deposited in bioresource centers, which have enabled us to perform positional cloning in rats. To date, more than 100 disease-related genes have been identified by positional cloning. Since some disease models are more accessible in rats than mice, the identification of causative genes in these models has sometimes led to the discovery of novel functions of genes. As before, various mutant rats are also expected to be discovered and developed as disease models in the future. Thus, the forward genetics continues to be an important approach to find genes involved in disease phenotypes in rats. In this review, I provide an overview the development of rat genome resources and describe examples of positional cloning in rats in which novel gene functions have been identified.
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Affiliation(s)
- Takashi Kuramoto
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan
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22
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Ramos A, Granzotto N, Kremer R, Boeder AM, de Araújo JFP, Pereira AG, Izídio GS. Hunting for Genes Underlying Emotionality in the Laboratory Rat: Maps, Tools and Traps. Curr Neuropharmacol 2023; 21:1840-1863. [PMID: 36056863 PMCID: PMC10514530 DOI: 10.2174/1570159x20666220901154034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/13/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
Scientists have systematically investigated the hereditary bases of behaviors since the 19th century, moved by either evolutionary questions or clinically-motivated purposes. The pioneer studies on the genetic selection of laboratory animals had already indicated, one hundred years ago, the immense complexity of analyzing behaviors that were influenced by a large number of small-effect genes and an incalculable amount of environmental factors. Merging Mendelian, quantitative and molecular approaches in the 1990s made it possible to map specific rodent behaviors to known chromosome regions. From that point on, Quantitative Trait Locus (QTL) analyses coupled with behavioral and molecular techniques, which involved in vivo isolation of relevant blocks of genes, opened new avenues for gene mapping and characterization. This review examines the QTL strategy applied to the behavioral study of emotionality, with a focus on the laboratory rat. We discuss the challenges, advances and limitations of the search for Quantitative Trait Genes (QTG) playing a role in regulating emotionality. For the past 25 years, we have marched the long journey from emotionality-related behaviors to genes. In this context, our experiences are used to illustrate why and how one should move forward in the molecular understanding of complex psychiatric illnesses. The promise of exploring genetic links between immunological and emotional responses are also discussed. New strategies based on humans, rodents and other animals (such as zebrafish) are also acknowledged, as they are likely to allow substantial progress to be made in the near future.
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Affiliation(s)
- André Ramos
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Natalli Granzotto
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rafael Kremer
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Ariela Maína Boeder
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Julia Fernandez Puñal de Araújo
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Aline Guimarães Pereira
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Geison Souza Izídio
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
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23
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Suber J, Zhang Y, Ye P, Guo R, Burks AW, Kulis MD, Smith SA, Iweala OI. Novel peanut-specific human IgE monoclonal antibodies enable screens for inhibitors of the effector phase in food allergy. Front Immunol 2022; 13:974374. [PMID: 36248809 PMCID: PMC9556733 DOI: 10.3389/fimmu.2022.974374] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background 10% of US residents have food allergies, including 2% with peanut allergy. Mast cell mediators released during the allergy effector phase drive allergic reactions. Therefore, targeting sensitized mast cells may prevent food allergy symptoms. Objective We used novel, human, allergen-specific, IgE monoclonal antibodies (mAbs) created using human hybridoma techniques to design an in vitro system to evaluate potential therapeutics targeting sensitized effector cells. Methods Two human IgE mAbs specific for peanut, generated through human hybridoma techniques, were used to sensitize rat basophilic leukemia (RBL) SX-38 cells expressing the human IgE receptor (FcϵRI). Beta-hexosaminidase release (a marker of degranulation), cytokine production, and phosphorylation of signal transduction proteins downstream of FcϵRI were measured after stimulation with peanut. Degranulation was also measured after engaging inhibitory receptors CD300a and Siglec-8. Results Peanut-specific human IgE mAbs bound FcϵRI, triggering degranulation after stimulation with peanut in RBL SX-38 cells. Sensitized RBL SX-38 cells stimulated with peanut increased levels of phosphorylated SYK and ERK, signal transduction proteins downstream of FcϵRI. Engaging inhibitory cell surface receptors CD300a or Siglec-8 blunted peanut-specific activation. Conclusion Allergen-specific human IgE mAbs, expressed from human hybridomas and specific for a clinically relevant food allergen, passively sensitize allergy effector cells central to the in vitro models of the effector phase of food allergy. Peanut reproducibly activates and induces degranulation of RBL SX-38 cells sensitized with peanut-specific human IgE mAbs. This system provides a unique screening tool to assess the efficacy of therapeutics that target allergy effector cells and inhibit food allergen-induced effector cell activation.
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Affiliation(s)
- Jada Suber
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, United States
- Department of Medicine, Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, United States
- Department of Pediatrics, Division of Allergy and Immunology, University of North Carolina Food Allergy Initiative, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Yugen Zhang
- Department of Medicine, Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, United States
| | - Ping Ye
- Department of Pediatrics, Division of Allergy and Immunology, University of North Carolina Food Allergy Initiative, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Rishu Guo
- Department of Pediatrics, Division of Allergy and Immunology, University of North Carolina Food Allergy Initiative, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - A. Wesley Burks
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, United States
- Department of Pediatrics, Division of Allergy and Immunology, University of North Carolina Food Allergy Initiative, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Michael D. Kulis
- Department of Pediatrics, Division of Allergy and Immunology, University of North Carolina Food Allergy Initiative, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Scott A. Smith
- Department of Medicine, and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, United States
| | - Onyinye I. Iweala
- Department of Medicine, Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC, United States
- Department of Pediatrics, Division of Allergy and Immunology, University of North Carolina Food Allergy Initiative, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- *Correspondence: Onyinye I. Iweala,
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24
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Trace Element Interactions, Inflammatory Signaling, and Male Sex Implicated in Reduced Growth Following Excess Oral Iron Supplementation in Pre-Weanling Rats. Nutrients 2022; 14:nu14193913. [PMID: 36235565 PMCID: PMC9571796 DOI: 10.3390/nu14193913] [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: 08/13/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Iron supplements are frequently provided to infants in high-income countries despite low incidence of iron deficiency. There is growing concern regarding adverse health and development outcomes of excess iron provision in early life. Excess iron may directly damage developing organs through the formation of reactive oxygen species, alter systemic inflammatory signaling, and/or dysregulate trace mineral metabolism. To better characterize the in vivo effects of excess iron on development, we utilized a pre-weanling rat pup model. Lewis rat litters were culled to eight pups (four males and four females) and randomly assigned to daily supplementation groups receiving either vehicle control (CON; 10% w/v sucrose solution) or ferrous sulfate (FS) iron at one of the following doses: 10, 30, or 90 mg iron/kg body weight—FS-10, FS-30, and FS-90, respectively—from postnatal day (PD) 2 through 9. FS-90 litters, but not FS-30 or FS-10, failed to thrive compared to CON litters and had smaller brains on PD 10. Among the groups, FS-90 liver iron levels were highest, as were white blood cell counts. Compared to CON, circulating MCP-1 and liver zinc were increased in FS-90 pups, whereas liver copper was decreased. Growth defects due to excess FS provision in pre-weanling rats may be related to liver injury, inflammation, and altered trace mineral metabolism.
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25
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Zhang P, Brinton LT, Gharghabi M, Sher S, Williams K, Cannon M, Walker JS, Canfield D, Beaver L, Cempre CB, Phillips H, Chen X, Yan P, Lehman A, Scherle P, Wang M, Vaddi K, Baiocchi R, Wang R, Sampath D, Alinari L, Blachly JS, Lapalombella R. Targeting OXPHOS de novo purine synthesis as the nexus of FLT3 inhibitor-mediated synergistic antileukemic actions. SCIENCE ADVANCES 2022; 8:eabp9005. [PMID: 36112677 PMCID: PMC9481139 DOI: 10.1126/sciadv.abp9005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 05/09/2023]
Abstract
Using a genome-wide CRISPR screen, we identified CDK9, DHODH, and PRMT5 as synthetic lethal partners with gilteritinib treatment in fms-like tyrosine kinase 3 (FLT3)-internal tandem duplication (ITD) acute myeloid leukemia (AML) and genetically and pharmacologically validated their roles in gilteritinib sensitivity. The presence of FLT3-ITD is associated with an increase in anaerobic glycolysis, rendering leukemia cells highly sensitive to inhibition of glycolysis. Supportive of this, our data show the enrichment of single guide RNAs targeting 28 glycolysis-related genes upon gilteritinib treatment, suggesting that switching from glycolysis to oxidative phosphorylation (OXPHOS) may represent a metabolic adaption of AML in gilteritinib resistance. CDK9i/FLT3i, DHODHi/FLT3i, and PRMT5i/FLT3i pairs mechanistically converge on OXPHOS and purine biosynthesis blockade, implying that targeting the metabolic functions of these three genes and/or proteins may represent attractive strategies to sensitize AML to gilteritinib treatment. Our findings provide the basis for maximizing therapeutic impact of FLT3-ITD inhibitors and a rationale for a clinical trial of these novel combinations.
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Affiliation(s)
- Pu Zhang
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Lindsey T. Brinton
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Mehdi Gharghabi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Steven Sher
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Katie Williams
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Matthew Cannon
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Janek S. Walker
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Daniel Canfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Larry Beaver
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Casey B. Cempre
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Hannah Phillips
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Xuyong Chen
- Center for Childhood Cancer and Blood Diseases, Hematology/Oncology and BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, OH, USA
| | - Pearlly Yan
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Amy Lehman
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | | | - Min Wang
- Prelude Therapeutics, Wilmington, DE, USA
| | - Kris Vaddi
- Prelude Therapeutics, Wilmington, DE, USA
| | - Robert Baiocchi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Diseases, Hematology/Oncology and BMT, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University, Columbus, OH, USA
| | - Deepa Sampath
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Lapo Alinari
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - James S. Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Leukemia Research Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH, USA
| | - Rosa Lapalombella
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Leukemia Research Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH, USA
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26
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Identification of Hypothalamic Long Noncoding RNAs Associated with Hypertension and the Behavior/Neurological Phenotype of Hypertensive ISIAH Rats. Genes (Basel) 2022; 13:genes13091598. [PMID: 36140769 PMCID: PMC9498762 DOI: 10.3390/genes13091598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play an important role in the control of many physiological and pathophysiological processes, including the development of hypertension and other cardiovascular diseases. Nonetheless, the understanding of the regulatory function of many lncRNAs is still incomplete. This work is a continuation of our earlier study on the sequencing of hypothalamic transcriptomes of hypertensive ISIAH rats and control normotensive WAG rats. It aims to identify lncRNAs that may be involved in the formation of the hypertensive state and the associated behavioral features of ISIAH rats. Interstrain differences in the expression of seven lncRNAs were validated by quantitative PCR. Differential hypothalamic expression of lncRNAs LOC100910237 and RGD1562890 between hypertensive and normotensive rats was shown for the first time. Expression of four lncRNAs (Snhg4, LOC100910237, RGD1562890, and Tnxa-ps1) correlated with transcription levels of many hypothalamic genes differentially expressed between ISIAH and WAG rats (DEGs), including genes associated with the behavior/neurological phenotype and hypertension. After functional annotation of these DEGs, it was concluded that lncRNAs Snhg4, LOC100910237, RGD1562890, and Tnxa-ps1 may be involved in the hypothalamic processes related to immune-system functioning and in the response to various exogenous and endogenous factors, including hormonal stimuli. Based on the functional enrichment analysis of the networks, an association of lncRNAs LOC100910237 and Tnxa-ps1 with retinol metabolism and an association of lncRNAs RGD1562890 and Tnxa-ps1 with type 1 diabetes mellitus are proposed for the first time. Based on a discussion, it is hypothesized that previously functionally uncharacterized lncRNA LOC100910237 is implicated in the regulation of hypothalamic processes associated with dopaminergic synaptic signaling, which may contribute to the formation of the behavioral/neurological phenotype and hypertensive state of ISIAH rats.
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27
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Dursun C, Kwitek AE, Bozdag S. PhenoGeneRanker: Gene and Phenotype Prioritization Using Multiplex Heterogeneous Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2950-2962. [PMID: 34283720 PMCID: PMC9704494 DOI: 10.1109/tcbb.2021.3098278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Uncovering genotype-phenotype relationships is a fundamental challenge in genomics. Gene prioritization is an important step for this endeavor to make a short manageable list from a list of thousands of genes coming from high-throughput studies. Network propagation methods are promising and state of the art methods for gene prioritization based on the premise that functionally related genes tend to be close to each other in the biological networks. Recently, we introduced PhenoGeneRanker, a network-propagation algorithm for multiplex heterogeneous networks. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p values of gene and phenotype ranks using random stratified sampling of seeds of genes and phenotypes based on their connectivity degree in the network. In this study, we introduce the PhenoGeneRanker Bioconductor package and its application to multi-omics rat genome datasets to rank hypertension disease-related genes and strains. We showed that PhenoGeneRanker performed better to rank hypertension disease-related genes using multiplex gene networks than aggregated gene networks. We also showed that PhenoGeneRanker performed better to rank hypertension disease-related strains using multiplex phenotype network than single or aggregated phenotype networks. We performed a rigorous hyperparameter analysis and, finally showed that Gene Ontology (GO) enrichment of statistically significant top-ranked genes resulted in hypertension disease-related GO terms.
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28
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Nutrigenetic Interaction of Spontaneously Hypertensive Rat Chromosome 20 Segment and High-Sucrose Diet Sensitizes to Metabolic Syndrome. Nutrients 2022; 14:nu14163428. [PMID: 36014934 PMCID: PMC9416443 DOI: 10.3390/nu14163428] [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: 07/21/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Several corresponding regions of human and mammalian genomes have been shown to affect sensitivity to the manifestation of metabolic syndrome via nutrigenetic interactions. In this study, we assessed the effect of sucrose administration in a newly established congenic strain BN.SHR20, in which a limited segment of rat chromosome 20 from a metabolic syndrome model, spontaneously hypertensive rat (SHR), was introgressed into Brown Norway (BN) genomic background. We mapped the extent of the differential segment and compared the genomic sequences of BN vs. SHR within the segment in silico. The differential segment of SHR origin in BN.SHR20 spans about 9 Mb of the telomeric portion of the short arm of chromosome 20. We identified non-synonymous mutations e.g., in ApoM, Notch4, Slc39a7, Smim29 genes and other variations in or near genes associated with metabolic syndrome in human genome-wide association studies. Male rats of BN and BN.SHR20 strains were fed a standard diet for 18 weeks (control groups) or 16 weeks of standard diet followed by 14 days of high-sucrose diet (HSD). We assessed the morphometric and metabolic profiles of all groups. Adiposity significantly increased only in BN.SHR20 after HSD. Fasting glycemia and the glucose levels during the oral glucose tolerance test were higher in BN.SHR20 than in BN groups, while insulin levels were comparable. The fasting levels of triacylglycerols were the highest in sucrose-fed BN.SHR20, both compared to the sucrose-fed BN and the control BN.SHR20. The non-esterified fatty acids and total cholesterol concentrations were higher in BN.SHR20 compared to their respective BN groups, and the HSD elicited an increase in non-esterified fatty acids only in BN.SHR20. In a new genetically defined model, we have isolated a limited genomic region involved in nutrigenetic sensitization to sucrose-induced metabolic disturbances.
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Ran Z, Yang J, Liu Y, Chen X, Ma Z, Wu S, Huang Y, Song Y, Gu Y, Zhao S, Fa M, Lu J, Chen Q, Cao Z, Li X, Sun S, Yang T. GlioMarker: An integrated database for knowledge exploration of diagnostic biomarkers in gliomas. Front Oncol 2022; 12:792055. [PMID: 36081550 PMCID: PMC9446481 DOI: 10.3389/fonc.2022.792055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 07/15/2022] [Indexed: 11/23/2022] Open
Abstract
Gliomas are the most frequent malignant and aggressive tumors in the central nervous system. Early and effective diagnosis of glioma using diagnostic biomarkers can prolong patients' lives and aid in the development of new personalized treatments. Therefore, a thorough and comprehensive understanding of the diagnostic biomarkers in gliomas is of great significance. To this end, we developed the integrated and web-based database GlioMarker (http://gliomarker.prophetdb.org/), the first comprehensive database for knowledge exploration of glioma diagnostic biomarkers. In GlioMarker, accurate information on 406 glioma diagnostic biomarkers from 1559 publications was manually extracted, including biomarker descriptions, clinical information, associated literature, experimental records, associated diseases, statistical indicators, etc. Importantly, we integrated many external resources to provide clinicians and researchers with the capability to further explore knowledge on these diagnostic biomarkers based on three aspects. (1) Obtain more ontology annotations of the biomarker. (2) Identify the relationship between any two or more components of diseases, drugs, genes, and variants to explore the knowledge related to precision medicine. (3) Explore the clinical application value of a specific diagnostic biomarker through online analysis of genomic and expression data from glioma cohort studies. GlioMarker provides a powerful, practical, and user-friendly web-based tool that may serve as a specialized platform for clinicians and researchers by providing rapid and comprehensive knowledge of glioma diagnostic biomarkers to subsequently facilitates high-quality research and applications.
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Affiliation(s)
- Zihan Ran
- Department of Research, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
- The Genius Medicine Consortium (TGMC), Shanghai, China
| | - Jingcheng Yang
- The Genius Medicine Consortium (TGMC), Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | - Yaqing Liu
- The Genius Medicine Consortium (TGMC), Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - XiuWen Chen
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Zijing Ma
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Shaobo Wu
- Department of Laboratory Medicine, Tinglin Hospital of Jinshan District, Shanghai, China
| | - Yechao Huang
- The Genius Medicine Consortium (TGMC), Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yueqiang Song
- The Genius Medicine Consortium (TGMC), Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yu Gu
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Shuo Zhao
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Mengqi Fa
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Jiangjie Lu
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Qingwang Chen
- The Genius Medicine Consortium (TGMC), Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zehui Cao
- The Genius Medicine Consortium (TGMC), Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaofei Li
- The Genius Medicine Consortium (TGMC), Shanghai, China
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Shanyue Sun
- The Genius Medicine Consortium (TGMC), Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Yang
- Department of Radiology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
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Genome-wide linkage analysis combined with genome sequencing in large families with intracranial aneurysms. Eur J Hum Genet 2022; 30:833-840. [PMID: 35228681 PMCID: PMC9259640 DOI: 10.1038/s41431-022-01059-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/15/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Rupture of an intracranial aneurysm (IA) leads to aneurysmal subarachnoid haemorrhage (ASAH), a severe type of stroke. Some rare variants that cause IA in families have been identified, but still, the majority of genetic causes, as well as the biological mechanisms of IA development and rupture, remain unknown. We aimed to identify rare, damaging variants for IA in three large Dutch families with multiple affected members with IA (N = 9, 11, and 6). By combining linkage analysis and genome sequencing (GS), we identified six rare and damaging variants for which all cases within one of the families were heterozygous. These variants were p.Tyr87Cys in SYCP1, p.Phe1077Leu in FMNL2, p.Thr754Lys in TBC1D2, p.Arg321His in ZNF782, p.Arg979Trp in CCDC180, and p.Val125Met in NCBP1. None of the variants showed association with IA status in a large cohort of 937 patients from the general IA patient population and 1046 controls. Gene expression in IA and cerebral artery tissue further prioritized FMNL2 and TBC1D2 as potential important players in IA pathophysiology. Further studies are needed to characterize the functional consequences of the identified variants and their role in the biological mechanisms of IA.
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Clark KC, Wagner VA, Holl KL, Reho JJ, Tutaj M, Smith JR, Dwinell MR, Grobe JL, Kwitek AE. Body Composition and Metabolic Changes in a Lyon Hypertensive Congenic Rat and Identification of Ercc6l2 as a Positional Candidate Gene. Front Genet 2022; 13:903971. [PMID: 35812759 PMCID: PMC9263446 DOI: 10.3389/fgene.2022.903971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/03/2022] [Indexed: 12/15/2022] Open
Abstract
Central obesity is genetically complex, and its exponential increase in the last decades have made it a critical public health issue. The Lyon Hypertensive (LH) rat is a well-characterized hypertensive model that also exhibits spontaneous and profound differences in body weight and adiposity, relative to its metabolically healthy control, the Lyon Normotensive (LN) rat. The mechanisms underlying the body weight differences between these strains are not well-understood, thus a congenic model (LH17LNa) was developed where a portion of the proximal arm of LN chromosome 17 is introgressed on the LH genomic background to assess the contribution of LN alleles on obesity features. Male and female LH17LNa rats were studied, but male congenics did not significantly differ from LH in this study. Female LH17LNa rats exhibited decreases in total body growth, as well as major alterations to their body composition and adiposity. The LH17LNa female rats also showed decreases in metabolic rate, and a reduction in food intake. The increased adiposity in the female LH17LNa rats was specific to abdominal white adipose tissue, and this phenomenon was further explained by significant hypertrophy in those adipocytes, with no evidence of adipocyte hyperplasia. Sequencing of the parental strains identified a novel frameshift mutation in the candidate gene Ercc6l2, which is involved in transcription-coupled DNA repair, and is implicated in premature aging. The discovery of the significance of Ercc6l2 in the context of female-specific adipocyte biology could represent a novel role of DNA repair failure syndromes in obesity pathogenesis.
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Affiliation(s)
- Karen C. Clark
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Valerie A. Wagner
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Katie L. Holl
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - John J. Reho
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Monika Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, United States
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jennifer R. Smith
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, United States
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, United States
- Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Melinda R. Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, United States
- Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Justin L. Grobe
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
- *Correspondence: Anne E. Kwitek, ; Justin L. Grobe,
| | - Anne E. Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
- Comprehensive Rodent Metabolic Phenotyping Core, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, United States
- Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, United States
- Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
- *Correspondence: Anne E. Kwitek, ; Justin L. Grobe,
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Li Q, Li X, Tian B, Chen L. Protective effect of pterostilbene in a streptozotocin-induced mouse model of Alzheimer's disease by targeting monoamine oxidase B. J Appl Toxicol 2022; 42:1777-1786. [PMID: 35665945 DOI: 10.1002/jat.4355] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/06/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease in elderly population. Pterostilbene (PTS) is a resveratrol analogue with neuroprotective activity. However, the biological mechanisms of PTS in AD progression are largely uncertain. An animal model of AD was established using streptozotocin (STZ)-treated C57BL/6J mice. Monoamine oxidase B (MAOB) expression was analyzed by bioinformatics analysis and detected by western blotting assay. The memory impairment was investigated by Morris water maze test. The levels of Tau hyperphosphorylation and death-related proteins were detected by western blotting analysis. The levels of amyloid β (Aβ)1-42 accumulation, oxidative stress-related markers (ROS, MDA, SOD and GSH), and inflammation-relative markers (TNF-α, IL-1β, IL-6 and p-NF-κB) were measured by ELISA. MAOB expression was increased in hippocampus of AD mice, and it was decreased by PTS. PTS attenuated STZ-induced body weight loss and memory impairment by regulating MAOB. PTS mitigated Aβ1-42 accumulation and Tau hyperphosphorylation by regulating MAOB in STZ-treated mice. PTS attenuated neuronal death by decreasing cleaved caspase-3 and Bax levels and increasing Bcl2 expression in hippocampus by regulating MAOB in STZ-treated mice. PTS weakened STZ-induced oxidative stress in hippocampus by decreasing ROS and MDA levels and increasing SOD and GSH levels by regulating MAOB. PTS protected against STZ-induced neuroinflammation in hippocampus by inhibiting TNF-α, IL-1β, IL-6 and p-NF-κB levels through regulating MAOB. In conclusion, PTS alleviates STZ-induced memory impairment, Aβ1-42 accumulation, Tau hyperphosphorylation, neuronal death, oxidative stress and inflammation by decreasing MAOB in AD mice, proving anti-AD potential of PTS.
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Affiliation(s)
- Qiushi Li
- Department of Neurology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Xidong Li
- Department of Neurology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Buxian Tian
- Department of Neurology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Long Chen
- Department of Anesthesiology, the First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
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Greenhalgh R, Holding ML, Orr TJ, Henderson JB, Parchman TL, Matocq MD, Shapiro MD, Dearing MD. Trio‐binned genomes of the woodrats
Neotoma bryanti
and
Neotoma lepida
reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing genes. Mol Ecol Resour 2022; 22:2713-2731. [DOI: 10.1111/1755-0998.13650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Robert Greenhalgh
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
| | - Matthew L. Holding
- Department of Natural Resources & Environmental ScienceUniversity of Nevada1664 North Virginia StreetRenoNevada89775USA
- Present address: Life Sciences InstituteUniversity of Michigan210 Washtenaw AvenueAnn ArborMichigan48109USA
| | - Teri J. Orr
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
- Department of BiologyNew Mexico State University1780 East University AvenueLas CrucesNew Mexico88003USA
| | - James B. Henderson
- Center for Comparative GenomicsCalifornia Academy of Sciences55 Music Concourse DriveSan FranciscoCalifornia94118USA
| | - Thomas L. Parchman
- Department of BiologyUniversity of NevadaReno1664 North Virginia StreetNevada89775USA
| | - Marjorie D. Matocq
- Department of Natural Resources & Environmental ScienceUniversity of Nevada1664 North Virginia StreetRenoNevada89775USA
| | - Michael D. Shapiro
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
| | - M. Denise Dearing
- School of Biological SciencesUniversity of Utah257 South 1400 EastSalt Lake CityUtah84112USA
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Preventive aerobic training preserves sympathovagal function and improves DNA repair capacity of peripheral blood mononuclear cells in rats with cardiomyopathy. Sci Rep 2022; 12:6422. [PMID: 35440673 PMCID: PMC9018832 DOI: 10.1038/s41598-022-09361-z] [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: 11/03/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
To evaluate the effect of preventive aerobic exercise training on sympathovagal function, cardiac function, and DNA repair capacity in a preclinical model of doxorubicin (DOX)-induced cardiomyopathy. Forty male Wistar-Kyoto rats were allocated into four groups (n = 10/group): D (DOX-treated) and C (controls) remained sedentary, and DT (DOX-trained) and CT (control-trained) performed aerobic training 4 days/week, during 4 weeks before exposure to DOX (4 mg/kg/week during 4 weeks) or saline solution. We evaluated cardiac function (echocardiography), hemodynamic and sympathovagal modulation (artery-femoral cannulation), cardiac troponin T levels, and DNA repair capacity (comet assay). Exercise training preserved ejection fraction (D: − 14.44% vs. DT: − 1.05%, p < 0.001), fractional shortening (D: − 8.96% vs. DT: − 0.27%, p = 0.025) and troponin T levels (D: 6.4 ± 3.6 vs. DT: 2.8 ± 1.7 ng/mL, p = 0.010). DOX increased heart rate variability (C: 27.7 ± 7.9 vs. D: 7.5 ± 2.2 ms2, p < 0.001) and induced sympathovagal dysfunction (LF/HF, C: 0.37 ± 0.15 vs. D: 0.15 ± 0.15, p = 0.036) through exacerbation of sympathetic function (LF, C: 0.22 ± 0.01 vs. D: 0.48 ± 0.24 Hz, p = 0.019). Peripheral mononuclear blood cells of DT animals presented lower residual DNA damage (D: 43.4 ± 8.4% vs. DT: 26 ± 3.4%, p = 0.003 after 1 h). Cardioprotective effects of preventive aerobic exercise training are mediated by preservation of sympathovagal function and improvement of DNA repair capacity of peripheral blood mononuclear cells.
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Powrózek T, Pigoń-Zając D, Mazurek M, Ochieng Otieno M, Rahnama-Hezavah M, Małecka-Massalska T. TNF-α Induced Myotube Atrophy in C2C12 Cell Line Uncovers Putative Inflammatory-Related lncRNAs Mediating Muscle Wasting. Int J Mol Sci 2022; 23:ijms23073878. [PMID: 35409236 PMCID: PMC8998797 DOI: 10.3390/ijms23073878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 12/10/2022] Open
Abstract
Background: Muscle atrophy is a complex catabolic condition developing under different inflammatory-related systemic diseases resulting in wasting of muscle tissue. While the knowledge of the molecular background of muscle atrophy has developed in recent years, how the atrophic conditions affect the long non-coding RNA (lncRNAs) machinery and the exact participation of the latter in the mediation of muscle loss are still unknown. The purpose of the study was to assess how inflammatory condition developing under the tumor necrosis factor alpha (TNF-α) treatment affects the lncRNAs’ expression in a mouse skeletal muscle cell line. Materials and method: A C2C12 mouse myoblast cell line was treated with TNF-α to develop atrophy, and inflammatory-related lncRNAs mediating muscle loss were identified. Bioinformatics was used to validate and analyze the discovered lncRNAs. The differences in their expression under different TNF-α concentrations and treatment times were investigated. Results: Five lncRNAs were identified in a discovery set as atrophy related and then validated. Three lncRNAs, Gm4117, Ccdc41os1, and 5830418P13Rik, were selected as being significant for inflammatory-related myotube atrophy. Dynamics changes in the expression of lncRNAs depended on both TNF-α concentration and treatment time. Bioinformatics analysis revealed the mRNA and miRNA target for selected lncRNAs and their putative involvement in the molecular processes related to muscle atrophy. Conclusions: The inflammatory condition developing in the myotube under the TNF-α treatment affects the alteration of lncRNAs’ expression pattern. Experimental and bioinformatics testing suggested the prospective role of lncRNAs in the mediation of muscle loss under an inflammatory state.
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Affiliation(s)
- Tomasz Powrózek
- Department of Human Physiology, Medical University of Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (T.M.-M.)
- Correspondence:
| | - Dominika Pigoń-Zając
- Department of Human Physiology, Medical University of Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (T.M.-M.)
| | - Marcin Mazurek
- Department of Human Physiology, Medical University of Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (T.M.-M.)
| | - Michael Ochieng Otieno
- Haematological Malignancies H12O Clinical Research Unit, Spanish National Cancer Research Centre, 28029 Madrid, Spain;
| | - Mansur Rahnama-Hezavah
- Chair and Department of Dental Surgery, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Teresa Małecka-Massalska
- Department of Human Physiology, Medical University of Lublin, 20-080 Lublin, Poland; (D.P.-Z.); (M.M.); (T.M.-M.)
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Huang S, Dou J, Li Z, Hu L, Yu Y, Wang Y. Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data. Genes (Basel) 2022; 13:genes13020358. [PMID: 35205403 PMCID: PMC8871965 DOI: 10.3390/genes13020358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Heat stress is one of the most severe challenges faced in livestock production in summer. Alternative splicing as an important post-transcriptional regulation is rarely studied in heat-stressed animals. Here, we performed and analyzed RNA-sequencing assays on the liver of Sprague-Dawley rats in control (22 °C, n = 5) and heat stress (4 °C for 120 min, H120; n = 5) groups, resulting in the identification of 636 differentially expressed genes. Identification analysis of the alternative splicing events revealed that heat stress-induced alternative splicing events increased by 20.18%. Compared with other types of alternative splicing events, the alternative start increased the most (43.40%) after heat stress. Twenty-eight genes were differentially alternatively spliced (DAS) between the control and H120 groups, among which Acly, Hnrnpd and mir3064 were also differentially expressed. For DAS genes, Srebf1, Shc1, Srsf5 and Ensa were associated with insulin, while Cast, Srebf1, Tmem33, Tor1aip2, Slc39a7 and Sqstm1 were enriched in the composition of the endoplasmic reticulum. In summary, our study conducts a comprehensive profile of alternative splicing in heat-stressed rats, indicating that alternative splicing is one of the molecular mechanisms of heat stress response in mammals and providing reference data for research on heat tolerance in mammalian livestock.
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Affiliation(s)
- Shangzhen Huang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Jinhuan Dou
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 100193, China
- Correspondence: (J.D.); (Y.W.)
| | - Zhongshu Li
- Agricultural College, Yanbian University, Yanji 133002, China;
| | - Lirong Hu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Ying Yu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Yachun Wang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
- Correspondence: (J.D.); (Y.W.)
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37
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Sadovska L, Auders J, Keiša L, Romanchikova N, Silamiķele L, Kreišmane M, Zayakin P, Takahashi S, Kalniņa Z, Linē A. Exercise-Induced Extracellular Vesicles Delay the Progression of Prostate Cancer. Front Mol Biosci 2022; 8:784080. [PMID: 35087866 PMCID: PMC8787363 DOI: 10.3389/fmolb.2021.784080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Increasing evidence suggests that regular physical exercise not only reduces the risk of cancer but also improves functional capacity, treatment efficacy and disease outcome in cancer patients. At least partially, these effects are mediated by the secretome of the tissues responding to exercise. The secreted molecules can be released in a carrier-free form or enclosed into extracellular vesicles (EVs). Several recent studies have shown that EVs are actively released into circulation during physical exercise. Here, we for the first time investigated the effects of exercise-induced EVs on the progression of cancer in an F344 rat model of metastatic prostate cancer. Although we did not observe a consistent increase in the circulating EV levels, RNA sequencing analysis demonstrated substantial changes in the RNA content of EVs collected before and immediately after forced wheel running exercise as well as differences between EVs from runners at resting state and sedentary rats. The major RNA biotype in EVs was mRNA, followed by miRNA and rRNA. Molecular functions of differentially expressed RNAs reflected various physiological processes including protein folding, metabolism and regulation of immune responses triggered by the exercise in the parental cells. Intravenous administration of exercise-induced EVs into F344 rats with orthotopically injected syngeneic prostate cancer cells PLS10, demonstrated reduction of the primary tumor volume by 35% and possibly—attenuation of lung metastases. Hence, our data provide the first evidence that exercise-induced EVs may modulate tumor physiology and delay the progression of cancer.
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Affiliation(s)
- Lilite Sadovska
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Jānis Auders
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | - Laura Keiša
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | | | - Laila Silamiķele
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Madara Kreišmane
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Pawel Zayakin
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Zane Kalniņa
- Laboratory Animal Core Facility, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Aija Linē
- Cancer Biomarker Group, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Faculty of Biology, University of Latvia, Riga, Latvia
- *Correspondence: Aija Linē,
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Kaldunski ML, Smith JR, Hayman GT, Brodie K, De Pons JL, Demos WM, Gibson AC, Hill ML, Hoffman MJ, Lamers L, Laulederkind SJF, Nalabolu HS, Thorat K, Thota J, Tutaj M, Tutaj MA, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. Mamm Genome 2021; 33:66-80. [PMID: 34741192 PMCID: PMC8570235 DOI: 10.1007/s00335-021-09932-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/21/2021] [Indexed: 01/21/2023]
Abstract
Model organism research is essential for discovering the mechanisms of human diseases by defining biologically meaningful gene to disease relationships. The Rat Genome Database (RGD, ( https://rgd.mcw.edu )) is a cross-species knowledgebase and the premier online resource for rat genetic and physiologic data. This rich resource is enhanced by the inclusion and integration of comparative data for human and mouse, as well as other human disease models including chinchilla, dog, bonobo, pig, 13-lined ground squirrel, green monkey, and naked mole-rat. Functional information has been added to records via the assignment of annotations based on sequence similarity to human, rat, and mouse genes. RGD has also imported well-supported cross-species data from external resources. To enable use of these data, RGD has developed a robust infrastructure of standardized ontologies, data formats, and disease- and species-centric portals, complemented with a suite of innovative tools for discovery and analysis. Using examples of single-gene and polygenic human diseases, we illustrate how data from multiple species can help to identify or confirm a gene as involved in a disease and to identify model organisms that can be studied to understand the pathophysiology of a gene or pathway. The ultimate aim of this report is to demonstrate the utility of RGD not only as the core resource for the rat research community but also as a source of bioinformatic tools to support a wider audience, empowering the search for appropriate models for human afflictions.
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Affiliation(s)
- M L Kaldunski
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J R Smith
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - G T Hayman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J L De Pons
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - W M Demos
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A C Gibson
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M L Hill
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M J Hoffman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - L Lamers
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J F Laulederkind
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - H S Nalabolu
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Thorat
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J Thota
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M A Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Vedi
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J Wang
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M R Dwinell
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A E Kwitek
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
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Ringwald M, Richardson JE, Baldarelli RM, Blake JA, Kadin JA, Smith C, Bult CJ. Mouse Genome Informatics (MGI): latest news from MGD and GXD. Mamm Genome 2021; 33:4-18. [PMID: 34698891 PMCID: PMC8913530 DOI: 10.1007/s00335-021-09921-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/01/2022]
Abstract
The Mouse Genome Informatics (MGI) database system combines multiple expertly curated community data resources into a shared knowledge management ecosystem united by common metadata annotation standards. MGI's mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease. MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information, and annotations of mouse models with human diseases. MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of the Gene Ontology and Disease Ontology and uses these ontologies as standard terminologies for annotation. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI's two major knowledgebases. Here, we highlight some of the recent changes and enhancements to MGD and GXD that have been implemented in response to changing needs of the biomedical research community and to improve the efficiency of expert curation. MGI can be accessed freely at http://www.informatics.jax.org .
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The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment. Arch Toxicol 2021; 95:3745-3775. [PMID: 34626214 PMCID: PMC8536636 DOI: 10.1007/s00204-021-03141-w] [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: 05/16/2021] [Accepted: 08/12/2021] [Indexed: 01/26/2023]
Abstract
Mechanism-based risk assessment is urged to advance and fully permeate into current safety assessment practices, possibly at early phases of drug safety testing. Toxicogenomics is a promising source of mechanisms-revealing data, but interpretative analysis tools specific for the testing systems (e.g. hepatocytes) are lacking. In this study, we present the TXG-MAPr webtool (available at https://txg-mapr.eu/WGCNA_PHH/TGGATEs_PHH/ ), an R-Shiny-based implementation of weighted gene co-expression network analysis (WGCNA) obtained from the Primary Human Hepatocytes (PHH) TG-GATEs dataset. The 398 gene co-expression networks (modules) were annotated with functional information (pathway enrichment, transcription factor) to reveal their mechanistic interpretation. Several well-known stress response pathways were captured in the modules, were perturbed by specific stressors and showed preservation in rat systems (rat primary hepatocytes and rat in vivo liver), with the exception of DNA damage and oxidative stress responses. A subset of 87 well-annotated and preserved modules was used to evaluate mechanisms of toxicity of endoplasmic reticulum (ER) stress and oxidative stress inducers, including cyclosporine A, tunicamycin and acetaminophen. In addition, module responses can be calculated from external datasets obtained with different hepatocyte cells and platforms, including targeted RNA-seq data, therefore, imputing biological responses from a limited gene set. As another application, donors' sensitivity towards tunicamycin was investigated with the TXG-MAPr, identifying higher basal level of intrinsic immune response in donors with pre-existing liver pathology. In conclusion, we demonstrated that gene co-expression analysis coupled to an interactive visualization environment, the TXG-MAPr, is a promising approach to achieve mechanistic relevant, cross-species and cross-platform evaluation of toxicogenomic data.
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Integrative Map of HIF1A Regulatory Elements and Variations. Genes (Basel) 2021; 12:genes12101526. [PMID: 34680921 PMCID: PMC8536025 DOI: 10.3390/genes12101526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022] Open
Abstract
Hypoxia-inducible factor (HIF) family of transcription factors (HIF1A, EPAS1, and HIF3A) are regulators of the cellular response to hypoxia. They have been shown to be involved in development of various diseases such as cancer, diabetes, and erythrocytosis. A complete map of connections between HIF family of genes with various omics types has not yet been developed. The main aim of the present analysis was to construct the integrative map of genomic elements associated with HIF1A gene and prioritize potentially deleterious variants. Various genomic databases and bioinformatics tools were used, including Ensembl, MirTarBase, STRING, Cytoscape, MethPrimer, CADD, SIFT, and UALCAN. Integrative HIF1A gene map was visualized and includes transcriptional and post-transcriptional regulators, downstream targets, and genetic variants. One CpG island overlaps transcription start site of the HIF1A gene. Out of over 450 missense variants, four have predicted deleterious effect on protein function by at least five bioinformatics tools. Currently there are 85 miRNAs reported to target HIF1A. HIF1A downstream targets include protein-coding genes, long noncoding RNAs, and microRNAs (hypoxamiRs). The study presents the first integration of heterogeneous molecular interactions associated with HIF1A gene enabling a holistic view of the gene and lays the groundwork for supplementing the data in the future.
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Chadaeva I, Ponomarenko P, Kozhemyakina R, Suslov V, Bogomolov A, Klimova N, Shikhevich S, Savinkova L, Oshchepkov D, Kolchanov NA, Markel A, Ponomarenko M. Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation. Animals (Basel) 2021; 11:2667. [PMID: 34573632 PMCID: PMC8465180 DOI: 10.3390/ani11092667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022] Open
Abstract
Belyaev's concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized in commercial colors of the domesticated fox that never occur in the wild and has been confirmed in a wide variety of pet breeds. Many human disease models involving animals allow to test drugs before human testing. Perhaps this is why investigators doing transcriptomic profiling of domestic versus wild animals have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes of tame and aggressive rats, identified their differentially expressed genes (DEGs), and, for the first time, applied principal component analysis to compare them with all the known DEGs of domestic versus wild animals that we could find. Two principal components, PC1 and PC2, respectively explained 67% and 33% of differential-gene-expression variance (hereinafter: log2 value) between domestic and wild animals. PC1 corresponded to multiple orthologous DEGs supported by homologs; these DEGs kept the log2 value sign from species to species and from tissue to tissue (i.e., a common domestication pattern). PC2 represented stand-alone homologous DEG pairs reversing the log2 value sign from one species to another and from tissue to tissue (i.e., representing intraspecific and interspecific variation).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (P.P.); (R.K.); (V.S.); (A.B.); (N.K.); (S.S.); (L.S.); (D.O.); (N.A.K.); (A.M.)
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Robert H, Ferguson L, Reins O, Greco T, Prins ML, Folkerts M. Rodent Estrous Cycle Monitoring Utilizing Vaginal Lavage: No Such Thing As a Normal Cycle. JOURNAL OF VISUALIZED EXPERIMENTS : JOVE 2021:10.3791/62884. [PMID: 34515690 PMCID: PMC9888307 DOI: 10.3791/62884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The current methodology establishes a reproducible, standardized, and cost-effective approach to monitoring the estrous cycle of female Sprague Dawley (SD) adolescent rats. This study demonstrates the complexity of hormonal cycles and the broad spectrum of understanding required to construct a reliable and valid monitoring technique. Through an in-depth examination of principal experimental design and procedural elements, this description of the cycle and its fundamental principles provides a framework for further understanding and deconstructs misconceptions for future replication. Along with an outline of the sample collection process employing vaginal lavage, the procedure describes the mechanism of data categorization into the four-stage model of proestrus, estrus, metestrus, and diestrus. These stages are characterized by a new proposed approach, utilizing the 4 categorizing determinants of vaginal fluid condition, cell type(s) present, cell arrangement, and cell quantity at the time of collection. Variations of each stage, favorable and unfavorable samples, the distinction between cyclicity and acyclicity, and graphic depictions of the collected categorizing components are presented alongside effective interpretive and organizational practices of the data. Overall, these tools allow for the publication of quantifiable data ranges for the first time, leading to the standardization of categorization factors upon replication.
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Affiliation(s)
- Hannah Robert
- Department of Neurosurgery, Brain Injury Research Center, UCLA, David Geffen School of Medicine
| | - Lindsay Ferguson
- Department of Neurosurgery, Brain Injury Research Center, UCLA, David Geffen School of Medicine
| | - Olivia Reins
- Department of Psychology, Pepperdine University, Seaver College
| | - Tiffany Greco
- Department of Neurosurgery, Brain Injury Research Center, UCLA, David Geffen School of Medicine
| | - Mayumi L. Prins
- Department of Neurosurgery, Brain Injury Research Center, UCLA, David Geffen School of Medicine
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Nishimura M, Daino K, Fukuda M, Tanaka I, Moriyama H, Showler K, Nishimura Y, Takabatake M, Kokubo T, Ishikawa A, Inoue K, Fukushi M, Kakinuma S, Imaoka T, Shimada Y. Development of mammary cancer in γ-irradiated F1 hybrids of susceptible Sprague-Dawley and resistant Copenhagen rats, with copy-number losses that pinpoint potential tumor suppressors. PLoS One 2021; 16:e0255968. [PMID: 34388197 PMCID: PMC8362979 DOI: 10.1371/journal.pone.0255968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/28/2021] [Indexed: 01/03/2023] Open
Abstract
Copenhagen rats are highly resistant to mammary carcinogenesis, even after treatment with chemical carcinogens and hormones; most studies indicate that this is a dominant genetic trait. To test whether this trait is also dominant after radiation exposure, we characterized the susceptibility of irradiated Copenhagen rats to mammary carcinogenesis, as well as its inheritance, and identified tumor-suppressor genes that, when inactivated or mutated, may contribute to carcinogenesis. To this end, mammary cancer-susceptible Sprague-Dawley rats, resistant Copenhagen rats, and their F1 hybrids were irradiated with 4 Gy of γ-rays, and tumor development was monitored. Copy-number variations and allelic imbalances of genomic DNA were studied using microarrays and PCR analysis of polymorphic markers. Gene expression was assessed by quantitative PCR in normal tissues and induced mammary cancers of F1 rats. Irradiated Copenhagen rats exhibited a very low incidence of mammary cancer. Unexpectedly, this resistance trait did not show dominant inheritance in F1 rats; rather, they exhibited intermediate susceptibility levels (i.e., between those of their parent strains). The susceptibility of irradiated F1 rats to the development of benign mammary tumors (i.e., fibroadenoma and adenoma) was also intermediate. Copy-number losses were frequently observed in chromosome regions 1q52-54 (24%), 2q12-15 (33%), and 3q31-42 (24%), as were focal (38%) and whole (29%) losses of chromosome 5. Some of these chromosomal regions exhibited allelic imbalances. Many cancer-related genes within these regions were downregulated in mammary tumors as compared with normal mammary tissue. Some of the chromosomal losses identified have not been reported previously in chemically induced models, implying a novel mechanism inherent to the irradiated model. Based on these findings, Sprague-Dawley × Copenhagen F1 rats offer a useful model for exploring genes responsible for radiation-induced mammary cancer, which apparently are mainly located in specific regions of chromosomes 1, 2, 3 and 5.
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Affiliation(s)
- Mayumi Nishimura
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Kazuhiro Daino
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Maki Fukuda
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Radiobiology for Children’s Health Research Group, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Ikuya Tanaka
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Radiobiology for Children’s Health Research Group, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Hitomi Moriyama
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Kaye Showler
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Radiobiology for Children’s Health Research Group, Research Center for Radiation Protection, National Institute of Radiological Sciences, Chiba, Japan
| | - Yukiko Nishimura
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Masaru Takabatake
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Toshiaki Kokubo
- Laboratory Animal and Genome Sciences Section, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Atsuko Ishikawa
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Kazumasa Inoue
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Masahiro Fukushi
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Tatsuhiko Imaoka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- * E-mail: (TI); (YS)
| | - Yoshiya Shimada
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan
- Department of Radiological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- * E-mail: (TI); (YS)
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Coding variants in mouse and rat model organisms: mousepost and ratpost. Mamm Genome 2021; 33:81-87. [PMID: 34313794 DOI: 10.1007/s00335-021-09898-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
Mice and rats are the most commonly used vertebrate model organisms in biomedical research. The availability of a reference genome in both animals combined with the deep sequencing of several doze of popular inbred lines also provides rich sequence variation data in these species. In some cases, such sequence variants can be linked directly to a distinctive phenotype. In previous work, we created the mouse and rat online searchable databases ("Mousepost" and "Ratpost") where small variant information for protein coding transcripts in mouse and rat inbred strains can be easily retrieved at the amino acid level. These tools are directly useful in forward genetics strategies or as a repository of existing sequence variations. Here, we perform a comparison between the "Mousepost" and "Ratpost" databases and we couple these two tools to a database of human sequence variants ClinVar. We investigated the level of redundancy and complementarity of known variants in protein coding transcripts and found that the large majority of variants is species-specific. However, a small set of positions is conserved in an inbred line between both species. We conclude that both databases are highly complementary, but this may change with further sequencing efforts in both species.
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Lydic R, Baghdoyan HA. Prefrontal Cortex Metabolome Is Modified by Opioids, Anesthesia, and Sleep. Physiology (Bethesda) 2021; 36:203-219. [PMID: 34159803 DOI: 10.1152/physiol.00043.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Obtundation of wakefulness caused by opioids and loss of wakefulness caused by anesthetics and sleep significantly alter concentrations of molecules comprising the prefrontal cortex (PFC) metabolome. Quantifying state-selective changes in the PFC metabolome is essential for advancing functional metabolomics. Diverse functions of the PFC suggest the PFC metabolome as a potential therapeutic entry point for countermeasures to state-selective autonomic dysfunction.
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Affiliation(s)
- Ralph Lydic
- Psychology, University of Tennessee, Knoxville, Tennessee.,Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Helen A Baghdoyan
- Psychology, University of Tennessee, Knoxville, Tennessee.,Oak Ridge National Laboratory, Oak Ridge, Tennessee
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The Cocaine and Oxycodone Biobanks, Two Repositories from Genetically Diverse and Behaviorally Characterized Rats for the Study of Addiction. eNeuro 2021; 8:ENEURO.0033-21.2021. [PMID: 33875455 PMCID: PMC8213442 DOI: 10.1523/eneuro.0033-21.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 11/21/2022] Open
Abstract
The rat oxycodone and cocaine biobanks contain samples that vary by genotypes (by using genetically diverse genotyped HS rats), phenotypes (by measuring addiction-like behaviors in an advanced SA model), timepoints (samples are collected longitudinally before, during, and after SA, and terminally at three different timepoints in the addiction cycle: intoxication, withdrawal, and abstinence or without exposure to drugs through age-matched naive rats), samples collected (organs, cells, biofluids, feces), preservation (paraformaldehyde-fixed, snap-frozen, or cryopreserved) and application (proteomics, transcriptomics, microbiomics, metabolomics, epigenetics, anatomy, circuitry analysis, biomarker discovery, etc.Substance use disorders (SUDs) are pervasive in our society and have substantial personal and socioeconomical costs. A critical hurdle in identifying biomarkers and novel targets for medication development is the lack of resources for obtaining biological samples with a detailed behavioral characterization of SUD. Moreover, it is nearly impossible to find longitudinal samples. As part of two ongoing large-scale behavioral genetic studies in heterogeneous stock (HS) rats, we have created two preclinical biobanks using well-validated long access (LgA) models of intravenous cocaine and oxycodone self-administration (SA) and comprehensive characterization of addiction-related behaviors. The genetic diversity in HS rats mimics diversity in the human population and includes individuals that are vulnerable or resilient to compulsive-like responding for cocaine or oxycodone. Longitudinal samples are collected throughout the experiment, before exposure to the drug, during intoxication, acute withdrawal, and protracted abstinence, and include naive, age-matched controls. Samples include, but are not limited to, blood plasma, feces and urine, whole brains, brain slices and punches, kidney, liver, spleen, ovary, testis, and adrenal glands. Three preservation methods (fixed in formaldehyde, snap-frozen, or cryopreserved) are used to facilitate diverse downstream applications such as proteomics, metabolomics, transcriptomics, epigenomics, microbiomics, neuroanatomy, biomarker discovery, and other cellular and molecular approaches. To date, >20,000 samples have been collected from over 1000 unique animals and made available free of charge to non-profit institutions through https://www.cocainebiobank.org/ and https://www.oxycodonebiobank.org/.
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Bencurova P, Baloun J, Hynst J, Oppelt J, Kubova H, Pospisilova S, Brazdil M. Dynamic miRNA changes during the process of epileptogenesis in an infantile and adult-onset model. Sci Rep 2021; 11:9649. [PMID: 33958654 PMCID: PMC8102630 DOI: 10.1038/s41598-021-89084-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
Temporal lobe epilepsy (TLE) is the most common epilepsy type. TLE onset in infancy aggravates features like severity, drug responsiveness, or development of comorbidities. These aggravations may arise from altered micro RNA (miRNA) expression specific to the early onset of the disease. Although the miRNA involvement in TLE is widely studied, the relationship between the onset-age and miRNA expression has not been addressed. Here, we investigated the miRNA profile of infantile and adult-onset TLE in rats combining sequencing and PCR. Since miRNA expression changes with the disease progression, we scrutinized miRNA dynamics across three stages: acute, latent, and chronic. We report that infantile-onset TLE leads to changes in the expression of fewer miRNAs across these stages. Interestingly, the miRNA profile in the acute stage of infantile-onset TLE overlaps in dysregulation of miR-132-5p, -205, and -211-3p with the chronic stage of the disease starting in adulthood. The analysis of putative targets linked the majority of dysregulated miRNAs with pathways involved in epilepsy. Our profiling uncovered miRNA expression characteristic for infantile and adulthood-onset epileptogenesis, suggesting the distinct biology underlying TLE in the onset age-dependent matter. Our results indicate the necessity of addressing the onset age as an important parameter in future epilepsy research.
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Affiliation(s)
- Petra Bencurova
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.412752.70000 0004 0608 7557Brno Epilepsy Center, Department of Neurology, St. Anne’s University Hospital and Medical Faculty of Masaryk University, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Baloun
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jakub Hynst
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jan Oppelt
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, 19104-6100 Philadelphia, PA USA
| | - Hana Kubova
- grid.418095.10000 0001 1015 3316Department of Developmental Epileptology, Institute of Physiology, Academy of Sciences Czech Republic, Videnska 1083, 14220 Prague, Czech Republic
| | - Sarka Pospisilova
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Milan Brazdil
- grid.10267.320000 0001 2194 0956CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic ,grid.412752.70000 0004 0608 7557Brno Epilepsy Center, Department of Neurology, St. Anne’s University Hospital and Medical Faculty of Masaryk University, Pekarska 53, 656 91 Brno, Czech Republic
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Chenouard V, Remy S, Tesson L, Ménoret S, Ouisse LH, Cherifi Y, Anegon I. Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models. Front Genet 2021; 12:615491. [PMID: 33959146 PMCID: PMC8093876 DOI: 10.3389/fgene.2021.615491] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The rat has been extensively used as a small animal model. Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years. This review covers the techniques and advances used to generate genetically engineered rat lines and their application to the development of rat models more broadly, such as conditional knockouts and reporter gene strains. In addition, genome-editing techniques that remain to be explored in the rat are discussed. The review also focuses more particularly on two areas in which extensive work has been done: human genetic diseases and immune system analysis. Models are thoroughly described in these two areas and highlight the competitive advantages of rat models over available corresponding mouse versions. The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects.
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Affiliation(s)
- Vanessa Chenouard
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- genOway, Lyon, France
| | - Séverine Remy
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Laurent Tesson
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Séverine Ménoret
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes Université, Nantes, France
| | - Laure-Hélène Ouisse
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | | | - Ignacio Anegon
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
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Emanetci E, Çakır T. Network-Based Analysis of Cognitive Impairment and Memory Deficits from Transcriptome Data. J Mol Neurosci 2021; 71:2415-2428. [PMID: 33713319 DOI: 10.1007/s12031-021-01807-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022]
Abstract
Aging is an inevitable process that negatively affects all living organisms and their vital functions. The brain is one of the most important organs in living beings and is primarily impacted by aging. The molecular mechanisms of learning, memory and cognition are altered over time, and the impairment in these mechanisms can lead to neurodegenerative diseases. Transcriptomics can be used to study these impairments to acquire more detailed information on the affected molecular mechanisms. Here we analyzed learning- and memory-related transcriptome data by mapping it on the organism-specific protein-protein interactome network. Subnetwork discovery algorithms were applied to discover highly dysregulated subnetworks, which were complemented with co-expression-based interactions. The functional analysis shows that the identified subnetworks are enriched with genes having roles in synaptic plasticity, gliogenesis, neurogenesis and cognition, which are reported to be related to memory and learning. With a detailed analysis, we show that the results from different subnetwork discovery algorithms or from different transcriptomic datasets can be successfully reconciled, leading to a memory-learning network that sheds light on the molecular mechanisms behind aging and memory-related impairments.
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Affiliation(s)
- Elif Emanetci
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
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