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Jaume G, Peeters T, Song AH, Pettit R, Williamson DFK, Oldenburg L, Vaidya A, de Brot S, Chen RJ, Thiran JP, Le LP, Gerber G, Mahmood F. AI-driven Discovery of Morphomolecular Signatures in Toxicology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604355. [PMID: 39091765 PMCID: PMC11291055 DOI: 10.1101/2024.07.19.604355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Early identification of drug toxicity is essential yet challenging in drug development. At the preclinical stage, toxicity is assessed with histopathological examination of tissue sections from animal models to detect morphological lesions. To complement this analysis, toxicogenomics is increasingly employed to understand the mechanism of action of the compound and ultimately identify lesion-specific safety biomarkers for which in vitro assays can be designed. However, existing works that aim to identify morphological correlates of expression changes rely on qualitative or semi-quantitative morphological characterization and remain limited in scale or morphological diversity. Artificial intelligence (AI) offers a promising approach for quantitatively modeling this relationship at an unprecedented scale. Here, we introduce GEESE, an AI model designed to impute morphomolecular signatures in toxicology data. Our model was trained to predict 1,536 gene targets on a cohort of 8,231 hematoxylin and eosin-stained liver sections from Rattus norvegicus across 127 preclinical toxicity studies. The model, evaluated on 2,002 tissue sections from 29 held-out studies, can yield pseudo-spatially resolved gene expression maps, which we correlate with six key drug-induced liver injuries (DILI). From the resulting 25 million lesion-expression pairs, we established quantitative relations between up and downregulated genes and lesions. Validation of these signatures against toxicogenomic databases, pathway enrichment analyses, and human hepatocyte cell lines asserted their relevance. Overall, our study introduces new methods for characterizing toxicity at an unprecedented scale and granularity, paving the way for AI-driven discovery of toxicity biomarkers.
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Affiliation(s)
- Guillaume Jaume
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
| | - Thomas Peeters
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Signal Processing Laboratory, EPFL, Lausanne, Switzerland
| | - Andrew H. Song
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
| | - Rowland Pettit
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Drew F. K. Williamson
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Lukas Oldenburg
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Anurag Vaidya
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA
| | - Simone de Brot
- Institute of Animal Pathology, Vetsuisse, University of Bern, Switzerland
- COMPATH, Institute of Animal Pathology, University of Bern, Switzerland
- Bern Center for Precision Medicine, University of Bern, Switzerland
| | - Richard J. Chen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
| | | | - Long Phi Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Harvard Data Science Initiative, Harvard University, Cambridge, MA
| | - Georg Gerber
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA
- Harvard Data Science Initiative, Harvard University, Cambridge, MA
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Oshchepkov DY, Makovka YV, Fedoseeva LA, Seryapina AA, Markel AL, Redina OE. Effect of Short-Term Restraint Stress on the Hypothalamic Transcriptome Profiles of Rats with Inherited Stress-Induced Arterial Hypertension (ISIAH) and Normotensive Wistar Albino Glaxo (WAG) Rats. Int J Mol Sci 2024; 25:6680. [PMID: 38928385 PMCID: PMC11203755 DOI: 10.3390/ijms25126680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/07/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Emotional stress is one of the health risk factors in the modern human lifestyle. Stress exposure can provoke the manifestation of various pathological conditions, one of which is a sharp increase in the blood pressure level. In the present study, we analyzed changes in the transcriptome profiles of the hypothalamus of hypertensive ISIAH and normotensive WAG rats exposed to a single short-term restraint stress (the rat was placed in a tight wire-mesh cage for 2 h). This type of stress can be considered emotional stress. The functional annotation of differentially expressed genes allowed us to identify the most significantly altered biological processes in the hypothalamus of hypertensive and normotensive rats. The study made it possible to identify a group of genes that describe a general response to stress, independent of the rat genotype, as well as a hypothalamic response to stress specific to each strain. The alternatively changing expression of the Npas4 (neuronal PAS domain protein 4) gene, which is downregulated in the hypothalamus of the control WAG rats and induced in the hypothalamus of hypertensive ISIAH rats, is suggested to be the key event for understanding inter-strain differences in the hypothalamic response to stress. The stress-dependent ISIAH strain-specific induction of Fos and Jun gene transcription may play a crucial role in neuronal activation in this rat strain. The data obtained can be potentially useful in the selection of molecular targets for the development of pharmacological approaches to the correction of stress-induced pathologies related to neuronal excitability, taking into account the hypertensive status of the patients.
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Affiliation(s)
- Dmitry Yu. Oshchepkov
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.Y.O.); (Y.V.M.); (L.A.F.); (A.A.S.); (A.L.M.)
- Kurchatov Genomic Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Yulia V. Makovka
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.Y.O.); (Y.V.M.); (L.A.F.); (A.A.S.); (A.L.M.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Larisa A. Fedoseeva
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.Y.O.); (Y.V.M.); (L.A.F.); (A.A.S.); (A.L.M.)
| | - Alisa A. Seryapina
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.Y.O.); (Y.V.M.); (L.A.F.); (A.A.S.); (A.L.M.)
| | - Arcady L. Markel
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.Y.O.); (Y.V.M.); (L.A.F.); (A.A.S.); (A.L.M.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga E. Redina
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.Y.O.); (Y.V.M.); (L.A.F.); (A.A.S.); (A.L.M.)
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Martins RS, Weber J, Johnson B, Luo J, Poulikidis K, Latif MJ, Razi SS, Al Shetawi AH, Lebovics RS, Bhora FY. Identifying Molecular Pathophysiology and Potential Therapeutic Options in Iatrogenic Tracheal Stenosis. Biomedicines 2024; 12:1323. [PMID: 38927530 PMCID: PMC11201234 DOI: 10.3390/biomedicines12061323] [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: 05/13/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION While most patients with iatrogenic tracheal stenosis (ITS) respond to endoscopic ablative procedures, approximately 15% experience a recalcitrant, recurring disease course that is resistant to conventional management. We aimed to explore genetic profiles of patients with recalcitrant ITS to understand underlying pathophysiology and identify novel therapeutic options. METHODS We collected 11 samples of granulation tissue from patients with ITS and performed RNA sequencing. We identified the top 10 most highly up- and down-regulated genes and cellular processes that these genes corresponded to. For the most highly dysregulated genes, we identified potential therapeutic options that favorably regulate their expression. RESULTS The dysregulations in gene expression corresponded to hyperkeratinization (upregulation of genes involved in keratin production and keratinocyte differentiation) and cellular proliferation (downregulation of cell cycle regulating and pro-apoptotic genes). Genes involved in retinoic acid (RA) metabolism and signaling were dysregulated in a pattern suggesting local cellular RA deficiency. Consequently, RA also emerged as the most promising potential therapeutic option for ITS, as it favorably regulated seven of the ten most highly dysregulated genes. CONCLUSION This is the first study to characterize the role of hyperkeratinization and dysregulations in RA metabolism and signaling in the disease pathophysiology. Given the ability of RA to favorably regulate key genes involved in ITS, future studies must explore its efficacy as a potential therapeutic option for patients with recalcitrant ITS.
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Affiliation(s)
- Russell Seth Martins
- Division of Thoracic Surgery, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA; (R.S.M.); (J.W.); (J.L.); (K.P.); (M.J.L.); (S.S.R.)
| | - Joanna Weber
- Division of Thoracic Surgery, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA; (R.S.M.); (J.W.); (J.L.); (K.P.); (M.J.L.); (S.S.R.)
| | - Bryan Johnson
- Department of Surgery, Mount Carmel Health System, Columbus, OH 43213, USA;
| | - Jeffrey Luo
- Division of Thoracic Surgery, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA; (R.S.M.); (J.W.); (J.L.); (K.P.); (M.J.L.); (S.S.R.)
| | - Kostantinos Poulikidis
- Division of Thoracic Surgery, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA; (R.S.M.); (J.W.); (J.L.); (K.P.); (M.J.L.); (S.S.R.)
| | - Mohammed Jawad Latif
- Division of Thoracic Surgery, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA; (R.S.M.); (J.W.); (J.L.); (K.P.); (M.J.L.); (S.S.R.)
| | - Syed Shahzad Razi
- Division of Thoracic Surgery, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA; (R.S.M.); (J.W.); (J.L.); (K.P.); (M.J.L.); (S.S.R.)
| | - Al Haitham Al Shetawi
- Division of Surgical Oncology, Department of Surgery, Vassar Brothers Medical Center, Nuvance Health, Dyson Center for Cancer Care, Poughkeepsie, NY 12601, USA;
- Division of Oral and Maxillofacial Surgery, Department of Surgery, Vassar Brothers Medical Center, Nuvance Health, Poughkeepsie, NY 12601, USA
| | - Robert S. Lebovics
- Division of Otolaryngology, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA;
| | - Faiz Y. Bhora
- Division of Thoracic Surgery, Department of Surgery, Hackensack Meridian School of Medicine, Hackensack Meridian Health (HMH) Network, Edison, NJ 08820, USA; (R.S.M.); (J.W.); (J.L.); (K.P.); (M.J.L.); (S.S.R.)
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4
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Nadiger N, Veed JK, Chinya Nataraj P, Mukhopadhyay A. DNA methylation and type 2 diabetes: a systematic review. Clin Epigenetics 2024; 16:67. [PMID: 38755631 PMCID: PMC11100087 DOI: 10.1186/s13148-024-01670-6] [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: 01/20/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVE DNA methylation influences gene expression and function in the pathophysiology of type 2 diabetes mellitus (T2DM). Mapping of T2DM-associated DNA methylation could aid early detection and/or therapeutic treatment options for diabetics. DESIGN A systematic literature search for associations between T2DM and DNA methylation was performed. Prospero registration ID: CRD42020140436. METHODS PubMed and ScienceDirect databases were searched (till October 19, 2023). Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and New Castle Ottawa scale were used for reporting the selection and quality of the studies, respectively. RESULT Thirty-two articles were selected. Four of 130 differentially methylated genes in blood, adipose, liver or pancreatic islets (TXNIP, ABCG1, PPARGC1A, PTPRN2) were reported in > 1 study. TXNIP was hypomethylated in diabetic blood across ethnicities. Gene enrichment analysis of the differentially methylated genes highlighted relevant disease pathways (T2DM, type 1 diabetes and adipocytokine signaling). Three prospective studies reported association of methylation in IGFBP2, MSI2, FTO, TXNIP, SREBF1, PHOSPHO1, SOCS3 and ABCG1 in blood at baseline with incident T2DM/hyperglycemia. Sex-specific differential methylation was reported only for HOOK2 in visceral adipose tissue (female diabetics: hypermethylated, male diabetics: hypomethylated). Gene expression was inversely associated with methylation status in 8 studies, in genes including ABCG1 (blood), S100A4 (adipose tissue), PER2 (pancreatic islets), PDGFA (liver) and PPARGC1A (skeletal muscle). CONCLUSION This review summarizes available evidence for using DNA methylation patterns to unravel T2DM pathophysiology. Further validation studies in diverse populations will set the stage for utilizing this knowledge for identifying early diagnostic markers and novel druggable pathways.
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Affiliation(s)
- Nikhil Nadiger
- Research Scholar, Manipal Academy of Higher Education, Manipal, India
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
| | - Jyothisha Kana Veed
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
| | - Priyanka Chinya Nataraj
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India
- Vedantu, Bangalore, India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's Medical College, St Johns National Academy of Health Sciences, Sarjapura Road, Koramangala, Bangalore, 560034, India.
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5
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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Cherry JM, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Gramates LS, Grove CA, Hale P, Harris T, Hayman GT, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Van Auken K, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources central infrastructure. Genetics 2024; 227:iyae049. [PMID: 38552170 PMCID: PMC11075569 DOI: 10.1093/genetics/iyae049] [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: 11/20/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024] Open
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).
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Affiliation(s)
| | | | | | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Susan M Bello
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Olin Blodgett
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | | | - Carol J Bult
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Brian R Calvi
- Department of Biology, Indiana University , Bloomington, IN 47408 , USA
| | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - J Michael Cherry
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Madeline A Crosby
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Jeffrey L De Pons
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | | | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Mary E Dolan
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gilberto dos Santos
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Dustin Ebert
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Stacia R Engel
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - David Fashena
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Malcolm Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University , 5000 Forbes Ave, Pittsburgh, PA 15203
| | - Adam C Gibson
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Varun R Gollapally
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - L Sian Gramates
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Paul Hale
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Todd Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - G Thomas Hayman
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Yanhui Hu
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Kalpana Karra
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Anne E Kwitek
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Stanley J F Laulederkind
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Raymond Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ian Longden
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Nicholas Markarian
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Beverley Matthews
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Monica S McAndrews
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Stuart Miyasato
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Howie Motenko
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Sierra Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Anushya Muruganujan
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Tremayne Mushayahama
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Robert S Nash
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Holly Paddock
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Troy Pells
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Norbert Perrimon
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christian Pich
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | | | | | - Susan Russo Gelbart
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Leyla Ruzicka
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - David R Shaw
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ajay Shrivatsav
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Amy Singer
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Constance M Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Cynthia L Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Jennifer R Smith
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Tabone
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Paul D Thomas
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Ketaki Thorat
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jyothi Thota
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Monika Tomczuk
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Vitor Trovisco
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Marek A Tutaj
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jose-Maria Urbano
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ceri E Van Slyke
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Shuai Weng
- Department of Genetics, Stanford University , Stanford, CA 94305
| | | | - Laurens G Wilming
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Edith D Wong
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Adam Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Pinglei Zhou
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Aaron Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Mark Zytkovicz
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
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6
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Siberski-Cooper CJ, Mayes MS, Gorden PJ, Kramer L, Bhatia V, Koltes JE. The genetic architecture of complete blood counts in lactating Holstein dairy cows. Front Genet 2024; 15:1360295. [PMID: 38601075 PMCID: PMC11004310 DOI: 10.3389/fgene.2024.1360295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024] Open
Abstract
Complete blood counts (CBCs) measure the abundance of individual immune cells, red blood cells, and related measures such as platelets in circulating blood. These measures can indicate the health status of an animal; thus, baseline circulating levels in a healthy animal may be related to the productive life, resilience, and production efficiency of cattle. The objective of this study is to determine the heritability of CBC traits and identify genomic regions that are associated with CBC measurements in lactating Holstein dairy cattle. The heritability of CBCs was estimated using a Bayes C0 model. The study population consisted of 388 cows with genotypes at roughly 75,000 markers and 16 different CBC phenotypes taken at one to three time points (n = 33, 131, and 224 for 1, 2, and 3 time points, respectively). Heritabilities ranged from 0.00 ± 0.00 (red cell distribution width) to 0.68 ± 0.06 (lymphocytes). A total of 96 different 1-Mb windows were identified that explained more than 1% of the genetic variance for at least one CBC trait, with 10 windows explaining more than 1% of the genetic variance for two or more traits. Multiple genes in the identified regions have functions related to immune response, cell differentiation, anemia, and disease. Positional candidate genes include RAD52 motif-containing protein 1 (RDM1), which is correlated with the degree of immune infiltration of immune cells, and C-X-C motif chemokine ligand 12 (CXCL12), which is critically involved in neutrophil bone marrow storage and release regulation and enhances neutrophil migration. Since animal health directly impacts feed intake, understanding the genetics of CBCs may be useful in identifying more disease-resilient and feed-efficient dairy cattle. Identification of genes responsible for variation in CBCs will also help identify the variability in how dairy cattle defend against illness and injury.
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Affiliation(s)
| | - Mary S. Mayes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Patrick J. Gorden
- Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Vishesh Bhatia
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
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7
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Noack D, van den Hout MCGN, Embregts CWE, van IJcken WFJ, Koopmans MPG, Rockx B. Species-specific responses during Seoul orthohantavirus infection in human and rat lung microvascular endothelial cells. PLoS Negl Trop Dis 2024; 18:e0012074. [PMID: 38536871 PMCID: PMC11020687 DOI: 10.1371/journal.pntd.0012074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/16/2024] [Accepted: 03/15/2024] [Indexed: 04/18/2024] Open
Abstract
Seoul orthohantavirus (SEOV) is a rat-borne zoonotic virus that is transmitted via inhalation of aerosolized infectious excreta, and can cause hemorrhagic fever with renal syndrome (HFRS) in humans worldwide. In rats, SEOV predominantly exists as a persistent infection in the absence of overt clinical signs. Lack of disease in rats is attributed to downregulation of pro-inflammatory and upregulation of regulatory host responses. As lung microvascular endothelial cells (LMECs) represent a primary target of infection in both human and rats, infections in these cells provide a unique opportunity to study the central role of LMECs in the dichotomy between pathogenicity in both species. In this study, host responses to SEOV infection in primary human and rat LMECs were directly compared on a transcriptional level. As infection of rat LMECs was more efficient than human LMECs, the majority of anti-viral defense responses were observed earlier in rat LMECs. Most prominently, SEOV-induced processes in both species included responses to cytokine stimulus, negative regulation of innate immune responses, responses to type I and II interferons, regulation of pattern recognition receptor signaling and MHC-I signaling. However, over time, in the rat LMECs, responses shifted from an anti-viral state towards a more immunotolerant state displayed by a PD-L1, B2M-, JAK2-focused interaction network aiding in negative regulation of cytotoxic CD8-positive T cell activation. This suggests a novel mechanism by which species-specific orthohantavirus-induced endothelium and T cell crosstalk may play a crucial role in the development of acute disease in humans and persistence in rodents.
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Affiliation(s)
- Danny Noack
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mirjam C. G. N. van den Hout
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Carmen W. E. Embregts
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
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8
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Mosalev KI, Ivanov ID, Tenditnik MV, Shults EE, Vavilin VA. Hepatotropic activity of a betulonic acid based compound. BIOMEDITSINSKAIA KHIMIIA 2024; 70:15-24. [PMID: 38450677 DOI: 10.18097/pbmc20247001015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Using the model of cyclophosphamide (CP)-induced immunosuppression in C57BL/6 mice, the hepatotropic effects of a conjugate of betulonic acid with 9-(4-methylpiperazin-1-ylmethyl)-2-(1,2,3-triazolyl) oreozelone (BABC) have been studied. In the liver of treated animals the expression of genes for cytochromes (CYP 1A1, CYP 1A2, CYP 3A44, CYP 2B10, CYP 2C29, CYP 17A1), PPARA, and cytokines (TNF-α, IL-1β, IL-12α, IL-10) and the relative levels of NF-κB p65, GST-π, and NAT-1 proteins were determined. On day six after administration of the compound and CP to animals a significant (3.2-fold) increase in the expression of the CYP 2B10 as compared to the control group was observed. Treatment of mice with the compound and CP also caused a 2.4-fold increase in the mRNA level of the pro-inflammatory TNF-α gene as compared to the group of animals receiving CP. Administration of the studied compound to intact animals was accompanied by a 2.5-fold increase in the IL-1β expression and a 1.8-fold decrease in the IL-10 expression as compared to the control group. An increase in the expression of pro-inflammatory cytokine genes in the liver of animals treated with the compound was accompanied by an increase in the content of NF-κB p65 (by 1.6 times), as well as an increase in the relative amount of NAT-1 protein (by 2.7 times) as compared to control animals.
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Affiliation(s)
- K I Mosalev
- Federal Research Center for Fundamental and Translational Medicine, Novosibirsk, Russia
| | - I D Ivanov
- Federal Research Center for Fundamental and Translational Medicine, Novosibirsk, Russia
| | - M V Tenditnik
- Research Institute of Neurosciences and Medicine, Novosibirsk, Russia
| | - E E Shults
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - V A Vavilin
- Federal Research Center for Fundamental and Translational Medicine, Novosibirsk, Russia
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9
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Flores CC, Pasetto NA, Wang H, Dimitrov A, Davis JF, Jiang Z, Davis CJ, Gerstner JR. Identification of sleep and circadian alternative polyadenylation sites associated with APA-linked human brain disorders. RESEARCH SQUARE 2024:rs.3.rs-3867797. [PMID: 38313253 PMCID: PMC10836116 DOI: 10.21203/rs.3.rs-3867797/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Sleep and circadian rhythm disruptions are comorbid features of many pathologies and can negatively influence numerous health conditions, including degenerative diseases, metabolic illnesses, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. Thus, associations between sleep and/or circadian rhythm and alternative polyadenylation (APA), particularly in the context of other health challenges, are largely undescribed. APA is a process that generates various transcript isoforms from the same gene, resulting in effects on mRNA translation, stability, localization, and subsequent function. Here, we have identified unique APAs in rat brain that exhibit time-of-day-dependent oscillations in expression as well as APAs that are altered by sleep deprivation and the subsequent recovery period. Genes affected by APA usage include Mapt/Tau, Ntrk2, Homer1A, Sin3band Sorl. Sorl1 has two APAs which cycle with a 24 h period, one additional APA cycles with a 12 h period and one more that is reduced during recovery sleep. Finally, we compared sleep- or circadian-associated APAs with recently described APA-linked brain disorder susceptibility genes and found 46 genes in common.
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10
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Badaczewska-Dawid AE, Kuriata A, Pintado-Grima C, Garcia-Pardo J, Burdukiewicz M, Iglesias V, Kmiecik S, Ventura S. A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms. Nucleic Acids Res 2024; 52:D360-D367. [PMID: 37897355 PMCID: PMC10767922 DOI: 10.1093/nar/gkad942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Protein aggregation has been associated with aging and different pathologies and represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed in Escherichia coli and other model organisms have allowed to dissect the biophysical principles underlying this process. This knowledge fuelled the development of computational tools, such as Aggrescan 3D (A3D) to forecast and re-design protein aggregation. Here, we present the A3D Model Organism Database (A3D-MODB) http://biocomp.chem.uw.edu.pl/A3D2/MODB, a comprehensive resource for the study of structural protein aggregation in the proteomes of 12 key model species spanning distant biological clades. In addition to A3D predictions, this resource incorporates information useful for contextualizing protein aggregation, including membrane protein topology and structural model confidence, as an indirect reporter of protein disorder. The database is openly accessible without any need for registration. We foresee A3D-MOBD evolving into a central hub for conducting comprehensive, multi-species analyses of protein aggregation, fostering the development of protein-based solutions for medical, biotechnological, agricultural and industrial applications.
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Affiliation(s)
| | - Aleksander Kuriata
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369, Białystok, Poland
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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11
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Bult CJ, Sternberg PW. The alliance of genome resources: transforming comparative genomics. Mamm Genome 2023; 34:531-544. [PMID: 37666946 PMCID: PMC10628019 DOI: 10.1007/s00335-023-10015-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023]
Abstract
Comparing genomic and biological characteristics across multiple species is essential to using model systems to investigate the molecular and cellular mechanisms underlying human biology and disease and to translate mechanistic insights from studies in model organisms for clinical applications. Building a scalable knowledge commons platform that supports cross-species comparison of rich, expertly curated knowledge regarding gene function, phenotype, and disease associations available for model organisms and humans is the primary mission of the Alliance of Genome Resources (the Alliance). The Alliance is a consortium of seven model organism knowledgebases (mouse, rat, yeast, nematode, zebrafish, frog, fruit fly) and the Gene Ontology resource. The Alliance uses a common set of gene ortholog assertions as the basis for comparing biological annotations across the organisms represented in the Alliance. The major types of knowledge associated with genes that are represented in the Alliance database currently include gene function, phenotypic alleles and variants, human disease associations, pathways, gene expression, and both protein-protein and genetic interactions. The Alliance has enhanced the ability of researchers to easily compare biological annotations for common data types across model organisms and human through the implementation of shared programmatic access mechanisms, data-specific web pages with a unified "look and feel", and interactive user interfaces specifically designed to support comparative biology. The modular infrastructure developed by the Alliance allows the resource to serve as an extensible "knowledge commons" capable of expanding to accommodate additional model organisms.
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12
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Okamoto F, Chitre AS, Missfeldt Sanches T, Chen D, Munro D, Polesskaya O, Palmer AA. Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.566473. [PMID: 38076923 PMCID: PMC10705385 DOI: 10.1101/2023.11.29.566473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Genome-wide association studies typically evaluate the autosomes and sometimes the X Chromosome, but seldom consider the Y or mitochondrial Chromosomes. We genotyped the Y and mitochondrial chromosomes in heterogeneous stock rats (Rattus norvegicus), which were created in 1984 by intercrossing eight inbred strains and have subsequently been maintained as an outbred population for 100 generations. As the Y and mitochondrial Chromosomes do not recombine, we determined which founder had contributed these chromosomes for each rat, and then performed association analysis for all complex traits (n=12,055; intersection of 12,116 phenotyped and 15,042 haplotyped rats). We found the eight founders had 8 distinct Y and 4 distinct mitochondrial Chromosomes, however only two of each were observed in our modern heterogeneous stock rat population (Generations 81-97). Despite the unusually large sample size, the p-value distribution did not deviate from expectations; there were no significant associations for behavioral, physiological, metabolome, or microbiome traits after correcting for multiple comparisons. However, both Y and mitochondrial Chromosomes were strongly associated with expression of a few genes located on those chromosomes, which provided a positive control. Our results suggest that within modern heterogeneous stock rats there are no Y and mitochondrial Chromosomes differences that strongly influence behavioral or physiological traits. These results do not address other ancestral Y and mitochondrial Chromosomes that do not appear in modern heterogeneous stock rats, nor do they address effects that may exist in other rat populations, or in other species.
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Affiliation(s)
- Faith Okamoto
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Apurva S Chitre
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Thiago Missfeldt Sanches
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Denghui Chen
- Bioinformatics and System Biology Program, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | | | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
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13
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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, Santos GD, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Auken KV, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567935. [PMID: 38045425 PMCID: PMC10690154 DOI: 10.1101/2023.11.20.567935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).
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14
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Thompson JM, Watts SW, Terrian L, Contreras GA, Rockwell C, Rendon CJ, Wabel E, Lockwood L, Bhattacharya S, Nault R. A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561581. [PMID: 37873456 PMCID: PMC10592719 DOI: 10.1101/2023.10.09.561581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. To examine the cell-specificity of recognized mechanotransducers we used single nuclei RNA sequencing (snRNAseq) of the thoracic aorta PVAT (taPVAT) from male Dahl SS rats compared to subscapular brown adipose tissue (BAT). Approximately 30,000 nuclei from taPVAT and BAT each were characterized by snRNAseq, identifying 8 major cell types expected and one unexpected (nuclei with oligodendrocyte marker genes). Cell-specific differential gene expression analysis between taPVAT and BAT identified up to 511 genes (adipocytes) with many (≥20%) being unique to individual cell types. Piezo1 was the most highly, widely expressed mechanotransducer. Presence of PIEZO1 in the PVAT was confirmed by RNAscope® and IHC; antagonism of PIEZO1 impaired the PVAT's ability to hold tension. Collectively, the cell compositions of taPVAT and BAT are highly similar, and PIEZO1 is likely a mechanotransducer in taPVAT.
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Affiliation(s)
- Janice M. Thompson
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
- Denotes individuals contributed equally as first authors to this work
| | - Stephanie W. Watts
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
- Denotes individuals contributed equally as first authors to this work
| | - Leah Terrian
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
- Denotes individuals contributed equally as first authors to this work
| | - G. Andres Contreras
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - Cheryl Rockwell
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - C. Javier Rendon
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - Emma Wabel
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - Lizabeth Lockwood
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - Sudin Bhattacharya
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Rance Nault
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
- Denotes individuals contributed equally as first authors to this work
- Denotes lead contact
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15
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Kim SJ, Affan RO, Frostig H, Scott BB, Alexander AS. Advances in cellular resolution microscopy for brain imaging in rats. NEUROPHOTONICS 2023; 10:044304. [PMID: 38076724 PMCID: PMC10704261 DOI: 10.1117/1.nph.10.4.044304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/23/2023] [Accepted: 11/07/2023] [Indexed: 02/12/2024]
Abstract
Rats are used in neuroscience research because of their physiological similarities with humans and accessibility as model organisms, trainability, and behavioral repertoire. In particular, rats perform a wide range of sophisticated social, cognitive, motor, and learning behaviors within the contexts of both naturalistic and laboratory environments. Further progress in neuroscience can be facilitated by using advanced imaging methods to measure the complex neural and physiological processes during behavior in rats. However, compared with the mouse, the rat nervous system offers a set of challenges, such as larger brain size, decreased neuron density, and difficulty with head restraint. Here, we review recent advances in in vivo imaging techniques in rats with a special focus on open-source solutions for calcium imaging. Finally, we provide suggestions for both users and developers of in vivo imaging systems for rats.
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Affiliation(s)
- Su Jin Kim
- Johns Hopkins University, Department of Psychological and Brain Sciences, Baltimore, Maryland, United States
| | - Rifqi O. Affan
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
- Boston University, Graduate Program in Neuroscience, Boston, Massachusetts, United States
| | - Hadas Frostig
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
| | - Benjamin B. Scott
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center and Photonics Center, Boston, Massachusetts, United States
| | - Andrew S. Alexander
- University of California Santa Barbara, Department of Psychological and Brain Sciences, Santa Barbara, California, United States
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