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Yuan H, Mancuso CA, Johnson K, Braasch I, Krishnan A. Computational strategies for cross-species knowledge transfer and translational biomedicine. ARXIV 2024:arXiv:2408.08503v1. [PMID: 39184546 PMCID: PMC11343225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that utilize transcriptome data and/or molecular networks. We introduce the term "agnology" to describe the functional equivalence of molecular components regardless of evolutionary origin, as this concept is becoming pervasive in integrative data-driven models where the role of evolutionary origin can become unclear. Our review addresses four key areas of information and knowledge transfer across species: (1) transferring disease and gene annotation knowledge, (2) identifying agnologous molecular components, (3) inferring equivalent perturbed genes or gene sets, and (4) identifying agnologous cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer.
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Affiliation(s)
- Hao Yuan
- Genetics and Genome Science Program; Ecology, Evolution, and Behavior Program, Michigan State University
| | - Christopher A. Mancuso
- Department of Biostatistics & Informatics, University of Colorado Anschutz Medical Campus
| | - Kayla Johnson
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus
| | - Ingo Braasch
- Department of Integrative Biology; Genetics and Genome Science Program; Ecology, Evolution, and Behavior Program, Michigan State University
| | - Arjun Krishnan
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus
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2
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Chen D, Chitre AS, Nguyen KMH, Cohen K, Peng B, Ziegler KS, Okamoto F, Lin B, Johnson BB, Sanches TM, Cheng R, Polesskaya O, Palmer AA. A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603984. [PMID: 39071405 PMCID: PMC11275765 DOI: 10.1101/2024.07.17.603984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Affordable sequencing and genotyping methods are essential for large scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, non-human model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping-by-sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping-by-sequencing and more recently generated by low-coverage whole-genome-sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21x coverage) and low-coverage whole-genome-sequencing data from 8,760 heterogeneous stock rats (mean 0.27x coverage), we can impute 7.32 million bi-allelic single-nucleotide polymorphisms with a concordance rate >99.76% compared to high-coverage (mean 33.26x coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping-by-sequencing or low-coverage whole-genome-sequencing for accurate genotyping, and demonstrate techniques that may also be useful for other genetic studies in non-human subjects.
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Affiliation(s)
- Denghui Chen
- Bioinformatics and System Biology Program, 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
| | - Khai-Minh H. Nguyen
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Katarina Cohen
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Beverly Peng
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Kendra S. Ziegler
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Faith Okamoto
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Bonnie Lin
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Benjamin B. Johnson
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Thiago M. Sanches
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093
| | - Riyan Cheng
- 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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3
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Hwang J, Lee HE, Han JS, Choi MH, Hong SH, Kim SW, Yang JH, Park U, Jung ES, Choi YJ. Sex-specific survival gene mutations are discovered as clinical predictors of clear cell renal cell carcinoma. Sci Rep 2024; 14:15800. [PMID: 38982123 PMCID: PMC11233666 DOI: 10.1038/s41598-024-66525-9] [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: 02/20/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Although sex differences have been reported in patients with clear cell renal cell carcinoma (ccRCC), biological sex has not received clinical attention and genetic differences between sexes are poorly understood. This study aims to identify sex-specific gene mutations and explore their clinical significance in ccRCC. We used data from The Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma (TCGA-KIRC), The Renal Cell Cancer-European Union (RECA-EU) and Korean-KIRC. A total of 68 sex-related genes were selected from TCGA-KIRC through machine learning, and 23 sex-specific genes were identified through verification using the three databases. Survival differences according to sex were identified in nine genes (ACSS3, ALG13, ASXL3, BAP1, JADE3, KDM5C, KDM6A, NCOR1P1, and ZNF449). Female-specific survival differences were found in BAP1 in overall survival (OS) (TCGA-KIRC, p = 0.004; RECA-EU, p = 0.002; and Korean-KIRC, p = 0.003) and disease-free survival (DFS) (TCGA-KIRC, p = 0.001 and Korean-KIRC, p = 0.000004), and NCOR1P1 in DFS (TCGA-KIRC, p = 0.046 and RECA-EU, p = 0.00003). Male-specific survival differences were found in ASXL3 (OS, p = 0.017 in TCGA-KIRC; and OS, p = 0.005 in RECA-EU) and KDM5C (OS, p = 0.009 in RECA-EU; and DFS, p = 0.016 in Korean-KIRC). These results suggest that biological sex may be an important predictor and sex-specific tailored treatment may improve patient care in ccRCC.
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Affiliation(s)
- Jia Hwang
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Hye Eun Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Jin Seon Han
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Moon Hyung Choi
- Department of Radiology, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, 03312, Republic of Korea
| | - Sung Hoo Hong
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Sae Woong Kim
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Ji Hoon Yang
- Department of Computer Science and Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Unsang Park
- Department of Computer Science and Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Eun Sun Jung
- Department of Hospital Pathology, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, 03312, Republic of Korea
| | - Yeong Jin Choi
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-Gu, Seoul, 06591, Republic of Korea.
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4
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Teboul L, Amos-Landgraf J, Benavides FJ, Birling MC, Brown SDM, Bryda E, Bunton-Stasyshyn R, Chin HJ, Crispo M, Delerue F, Dobbie M, Franklin CL, Fuchtbauer EM, Gao X, Golzio C, Haffner R, Hérault Y, Hrabe de Angelis M, Lloyd KCK, Magnuson TR, Montoliu L, Murray SA, Nam KH, Nutter LMJ, Pailhoux E, Pardo Manuel de Villena F, Peterson K, Reinholdt L, Sedlacek R, Seong JK, Shiroishi T, Smith C, Takeo T, Tinsley L, Vilotte JL, Warming S, Wells S, Whitelaw CB, Yoshiki A, Pavlovic G. Improving laboratory animal genetic reporting: LAG-R guidelines. Nat Commun 2024; 15:5574. [PMID: 38956430 PMCID: PMC11220107 DOI: 10.1038/s41467-024-49439-y] [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: 02/12/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals' genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.
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Affiliation(s)
- Lydia Teboul
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK.
| | - James Amos-Landgraf
- University of Missouri School of Medicine, Columbia, MO, USA
- University of Missouri College of Veterinary Medicine, Columbia, MO, USA
- Rat Resource and Research Center, University of Missouri, Columbia, MO, USA
| | - Fernando J Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
| | - Steve D M Brown
- Visiting Scientist, Institut Clinique de la Souris, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
| | - Elizabeth Bryda
- Rat Resource and Research Center, University of Missouri, Columbia, MO, 65201, USA
| | | | - Hsian-Jean Chin
- National Laboratory Animal Center (NLAC), NARLabs, Taipei, Taiwan
| | - Martina Crispo
- Laboratory Animal Biotechnology Unit, Institut Pasteur de Montevideo, Mataojo 2020, CP 1400, Montevideo, Uruguay
| | - Fabien Delerue
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Dobbie
- Phenomics Australia, Australian National University, 131 Garran Road, Canberra, ACT 2601, Australia
| | - Craig L Franklin
- University of Missouri Mutant Mouse Resource and Research Center (MU MMRRC), University of Missouri, Columbia, MO, 65201, USA
| | | | - Xiang Gao
- National Resource Center of Mutant Mice (NRCMM), Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Christelle Golzio
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, F-67400, Illkirch, France
| | - Rebecca Haffner
- Department Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yann Hérault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France
- Université de Strasbourg, CNRS, Inserm, IGBMC UMR 7104- UMR-S 1258, F-67400, Illkirch, France
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany
- German Center for Diabetes Research (DZD), Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
| | | | - Terry R Magnuson
- Department of Genetics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7264, USA
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), 28029, Madrid, Spain
| | | | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Lauryl M J Nutter
- Genetics and Genome Biology, The Hospital for Sick Children and The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
| | - Eric Pailhoux
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | | | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, and Korea Mouse Phenotyping Center, Seoul, 08826, Republic of Korea
| | | | - Cynthia Smith
- Mouse Genome Informatics (MGI), Jackson Laboratory, Bar Harbor, ME, USA
| | - Toru Takeo
- Center for Animal Resources and Development (CARD), Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Louise Tinsley
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
| | - Jean-Luc Vilotte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Søren Warming
- Genentech, Inc., a member of the Roche group, South San Francisco, CA, USA
| | - Sara Wells
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Didcot, OX11 0RD, Oxon, UK
- Francis Crick Institute, London, NW1 1AT, UK
| | - C Bruce Whitelaw
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France.
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5
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Yuan DY, McKeague ML, Raghu VK, Schoen RE, Finn OJ, Benos PV. Cellular and transcriptional profiles of peripheral blood mononuclear cells pre-vaccination predict immune response to preventative MUC1 vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598031. [PMID: 38948837 PMCID: PMC11212910 DOI: 10.1101/2024.06.14.598031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
A single arm trial (NCT007773097) and a double-blind, placebo controlled randomized trial ( NCT02134925 ) were conducted in individuals with a history of advanced colonic adenoma to test the safety and immunogenicity of the MUC1 tumor antigen vaccine and its potential to prevent new adenomas. These were the first two trials of a non-viral cancer vaccine administered in the absence of cancer. The vaccine was safe and strongly immunogenic in 43% (NCT007773097) and 25% ( NCT02134925 ) of participants. The lack of response in a significant number of participants suggested, for the first time, that even in a premalignant setting, the immune system may have already been exposed to some level of suppression previously reported only in cancer. Single-cell RNA-sequencing (scRNA-seq) on banked pre-vaccination peripheral blood mononuclear cells (PBMCs) from 16 immune responders and 16 non-responders identified specific cell types, genes, and pathways of a productive vaccine response. Responders had a significantly higher percentage of CD4+ naive T cells pre-vaccination, but a significantly lower percentage of CD8+ T effector memory (TEM) cells and CD16+ monocytes. Differential gene expression (DGE) and transcription factor inference analysis showed a higher level of expression of T cell activation genes, such as Fos and Jun, in CD4+ naive T cells, and pathway analysis showed enriched signaling activity in responders. Furthermore, Bayesian network analysis suggested that these genes were mechanistically connected to response. Our analyses identified several immune mechanisms and candidate biomarkers to be further validated as predictors of immune responses to a preventative cancer vaccine that could facilitate selection of individuals likely to benefit from a vaccine or be used to improve vaccine responses.
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6
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Aneli S, Ceccatelli Berti C, Gilea AI, Birolo G, Mutti G, Pavesi A, Baruffini E, Goffrini P, Capelli C. Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae. Hum Mol Genet 2024; 33:1152-1163. [PMID: 38558123 DOI: 10.1093/hmg/ddae057] [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: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, Turin 10126, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Via Santena 5, Turin 10126, Italy
| | - Giacomo Mutti
- Barcelona Supercomputing Centre (BSC-CNS), Department of Life Sciences, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Department of Mechanisms of Disease, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, United Kingdom
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7
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Miyakawa-Liu M, Ozawa MG, Chen M, Rahman M. A Novel Gene Fusion YLPM1::PRKD1 Identified in a Cribriform Subtype of Polymorphous Adenocarcinoma. Head Neck Pathol 2024; 18:43. [PMID: 38735907 PMCID: PMC11089030 DOI: 10.1007/s12105-024-01648-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024]
Abstract
Cribriform adenocarcinoma of the salivary gland (CASG) is an entity that is currently classified under polymorphous adenocarcinoma (PAC), cribriform subtype per the 2022 WHO classification of head and neck tumours. There is debate about whether CASG should be considered a separate diagnostic entity, as CASG differs from conventional PAC in anatomic site, clinical behaviors, and molecular patterns. Herein we describe a challenging and unique case which shares histologic and behavioral features between CASG and conventional PAC with a YLPM1::PRKD1 rearrangement not previously reported in the literature.
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Affiliation(s)
- Monica Miyakawa-Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, USA.
| | - Michael G Ozawa
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | - Michelle Chen
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Mobeen Rahman
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
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8
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Sternberg PW, Van Auken K, Wang Q, Wright A, Yook K, Zarowiecki M, Arnaboldi V, Becerra A, Brown S, Cain S, Chan J, Chen WJ, Cho J, Davis P, Diamantakis S, Dyer S, Grigoriadis D, Grove CA, Harris T, Howe K, Kishore R, Lee R, Longden I, Luypaert M, Müller HM, Nuin P, Quinton-Tulloch M, Raciti D, Schedl T, Schindelman G, Stein L. WormBase 2024: status and transitioning to Alliance infrastructure. Genetics 2024; 227:iyae050. [PMID: 38573366 PMCID: PMC11075546 DOI: 10.1093/genetics/iyae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024] Open
Abstract
WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.
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Affiliation(s)
- Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - 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
| | - Magdalena Zarowiecki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stephanie Brown
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - 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
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | | | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Todd Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Raymond Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ian Longden
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Hans-Michael Müller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
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9
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Baldarelli RM, Smith CL, Ringwald M, Richardson JE, Bult CJ. Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse. Genetics 2024; 227:iyae031. [PMID: 38531069 PMCID: PMC11075557 DOI: 10.1093/genetics/iyae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/13/2024] [Indexed: 03/28/2024] Open
Abstract
Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic and genomic aspects of human biology and disease using the laboratory mouse as a model system. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are core MGI databases that share data and system architecture. MGI serves as the central community resource of integrated information about mouse genome features, variation, expression, gene function, phenotype, and human disease models acquired from peer-reviewed publications, author submissions, and major bioinformatics resources. To facilitate integration and standardization of data, biocuration scientists annotate using terms from controlled metadata vocabularies and biological ontologies (e.g. Mammalian Phenotype Ontology, Mouse Developmental Anatomy, Disease Ontology, Gene Ontology, etc.), and by applying international community standards for gene, allele, and mouse strain nomenclature. MGI serves basic scientists, translational researchers, and data scientists by providing access to FAIR-compliant data in both human-readable and compute-ready formats. The MGI resource is accessible at https://informatics.jax.org. Here, we present an overview of the core data types represented in MGI and highlight recent enhancements to the resource with a focus on new data and functionality for MGD and GXD.
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Affiliation(s)
| | | | | | | | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
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10
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Öztürk-Çolak A, Marygold SJ, Antonazzo G, Attrill H, Goutte-Gattat D, Jenkins VK, Matthews BB, Millburn G, dos Santos G, Tabone CJ. FlyBase: updates to the Drosophila genes and genomes database. Genetics 2024; 227:iyad211. [PMID: 38301657 PMCID: PMC11075543 DOI: 10.1093/genetics/iyad211] [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: 10/17/2023] [Accepted: 11/27/2023] [Indexed: 02/03/2024] Open
Abstract
FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction of single-cell RNA sequencing data, improved content and display of functional information, updated orthology pipelines, new chemical reports, and enhancements to our outreach resources.
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Affiliation(s)
- Arzu Öztürk-Çolak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Damien Goutte-Gattat
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Victoria K Jenkins
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Beverley B Matthews
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Gilberto dos Santos
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Tabone
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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11
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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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12
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively parallel reporter assay confirms regulatory potential of hQTLs and reveals important variants in lupus and other autoimmune diseases. HGG ADVANCES 2024; 5:100279. [PMID: 38389303 PMCID: PMC10943488 DOI: 10.1016/j.xhgg.2024.100279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele-dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared with other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies in primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships among genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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13
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Messias TS, Silva KCP, Silva TC, Soares S. Potential of Viruses as Environmental Etiological Factors for Non-Syndromic Orofacial Clefts. Viruses 2024; 16:511. [PMID: 38675854 PMCID: PMC11053622 DOI: 10.3390/v16040511] [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: 02/08/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we analyzed the potential of viral infections in the species Homo sapiens as environmental causes of orofacial clefts (OFCs). A scoring system was adapted for qualitatively assessing the potential of viruses to cause cleft lip and/or palate (CL/P). This assessment considered factors such as information from the literature, nucleotide and amino acid similarities, and the presence of Endogenous Viral Elements (EVEs). The analysis involved various algorithm packages within Basic Local Alignment Search Tool 2.13.0 software and databases from the National Center for Biotechnology Information and the International Committee on Taxonomy of Viruses. Twenty significant viral species using different biosynthesis strategies were identified: Human coronavirus NL63, Rio Negro virus, Alphatorquevirus homin9, Brisavirus, Cosavirus B, Torque teno mini virus 4, Bocaparvovirus primate2, Human coronavirus HKU1, Monkeypox virus, Mammarenavirus machupoense, Volepox virus, Souris mammarenavirus, Gammapapillomavirus 7, Betainfluenzavirus influenzae, Lymphocytic choriomeningitis mammarenavirus, Ledantevirus kern, Gammainfluenzavirus influenzae, Betapolyomavirus hominis, Vesiculovirus perinet, and Cytomegalovirus humanbeta5. The evident viral etiological potential in relation to CL/P varies depending on the Baltimore class to which the viral species belongs. Given the multifactorial nature of CL/P, this relationship appears to be dynamic.
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Affiliation(s)
- Thiago S. Messias
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
| | - Kaique C. P. Silva
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
- Faculty of Medicine, Nove de Julho University, Bauru 17011-102, SP, Brazil
| | - Thiago C. Silva
- Faculty of Architecture, Arts, Communication and Design, São Paulo State University, Bauru 17033-360, SP, Brazil;
| | - Simone Soares
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
- Department of Prosthodontics and Periodontology, Bauru School of Dentistry, University of São Paulo, 9-75, Bauru 17012-901, SP, Brazil
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14
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Wright A, Wilkinson MD, Mungall C, Cain S, Richards S, Sternberg P, Provin E, Jacobs JL, Geib S, Raciti D, Yook K, Stein L, Molik DC. FAIR Header Reference genome: a TRUSTworthy standard. Brief Bioinform 2024; 25:bbae122. [PMID: 38555475 PMCID: PMC10981671 DOI: 10.1093/bib/bbae122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 04/02/2024] Open
Abstract
The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability and Technology. The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
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Affiliation(s)
- Adam Wright
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Mark D Wilkinson
- Departamento de Biotecnolog’ıa-Biolog’ıa Vegetal, Escuela T’ecnica Superior de Ingenier’ıa Agron’omica, Alimentaria y de Biosistemas,Centro de Biotecnolog’ıa y Gen’omica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Polit’ecnica de Madrid (UPM) - Instituto Nacional de Investigaci’on y Tecnolog’ıa Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarc’on, Madrid, ES, Spain
| | - Christopher Mungall
- Biosystems Data Science, Lawrence Berkeley National Laboratory, Building: 977, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Scott Cain
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS: BCM226, Houston, TX 77030, USA
| | - Paul Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ellen Provin
- Department of Horticultural Studies, Texas A&M University, HFSB 204, TAMU 2133, College Station, TX 77848, USA
| | - Jonathan L Jacobs
- American Type Culture Collection, 10801 University Blvd, Manassas, VA 20110, USA
| | - Scott Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo HI 96720, USA
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lincoln Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, 661 University Avenue Suite 500, Toronto, ON M5G 0A3, Canada
| | - David C Molik
- Arthropod-borne Animal Diseases Research Unit, Center for Grain and Animal Health Research United States Department of Agriculture, Agricultural Research Service, 1515 College Ave, Manhattan, KS 66502 USA
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15
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Franziscus CA, Ritz D, Kappel NC, Solinger JA, Schmidt A, Spang A. The protein tyrosine phosphatase PPH-7 is required for fertility and embryonic development in C. elegans at elevated temperatures. FEBS Open Bio 2024; 14:390-409. [PMID: 38320757 PMCID: PMC10909979 DOI: 10.1002/2211-5463.13771] [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: 08/11/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 03/05/2024] Open
Abstract
Post-translational modifications are key in the regulation of activity, structure, localization, and stability of most proteins in eukaryotes. Phosphorylation is potentially the most studied post-translational modification, also due to its reversibility and thereby the regulatory role this modification often plays. While most research attention was focused on kinases in the past, phosphatases remain understudied, most probably because the addition and presence of the modification is more easily studied than its removal and absence. Here, we report the identification of an uncharacterized protein tyrosine phosphatase PPH-7 in C. elegans, a member of the evolutionary conserved PTPN family of phosphatases. Lack of PPH-7 function led to reduction of fertility and embryonic lethality at elevated temperatures. Proteomics revealed changes in the regulation of targets of the von Hippel-Lindau (VHL) E3 ligase, suggesting a potential role for PPH-7 in the regulation of VHL.
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Affiliation(s)
| | | | | | | | | | - Anne Spang
- BiozentrumUniversity of BaselSwitzerland
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16
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Flores-Oropeza MA, Ochoa SA, Cruz-Córdova A, Chavez-Tepecano R, Martínez-Peñafiel E, Rembao-Bojórquez D, Zavala-Vega S, Hernández-Castro R, Flores-Encarnacion M, Arellano-Galindo J, Vélez D, Xicohtencatl-Cortes J. Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection. Front Microbiol 2024; 14:1340427. [PMID: 38328583 PMCID: PMC10848155 DOI: 10.3389/fmicb.2023.1340427] [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: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Recurrent urinary tract infections (RUTIs) caused by uropathogenic Escherichia coli are costly public health problems impacting patients' quality of life. Aim In this work, a comparative genomics analysis of three clinical RUTI strains isolated from bladder biopsy specimens was performed. Materials and methods One hundred seventy-two whole genomes of urinary tract E. coli strains were selected from the NCBI database. The search for virulence factors, fitness genes, regions of interest, and genetic elements associated with resistance was manually carried out. The phenotypic characterization of antibiotic resistance, haemolysis, motility, and biofilm formation was performed. Moreover, adherence and invasion assays with human bladder HTB-5 cells, and transmission electron microscopy (TEM) were performed. Results The UTI-1_774U and UTI-3_455U/ST1193 strains were associated with the extraintestinal pathotypes, and the UTI-2_245U/ST295 strain was associated with the intestinal pathotype, according to a phylogenetic analysis of 172 E. coli urinary strains. The three RUTI strains were of clinical, epidemiological, and zoonotic relevance. Several resistance genes were found within the plasmids of these strains, and a multidrug resistance phenotype was revealed. Other virulence genes associated with CFT073 were not identified in the three RUTI strains (genes for type 1 and P fimbriae, haemolysin hlyA, and sat toxin). Quantitative adherence analysis showed that UTI-1_774U was significantly (p < 0.0001) more adherent to human bladder HTB-5 cells. Quantitative invasion analysis showed that UTI-2_245U was significantly more invasive than the control strains. No haemolysis or biofilm activity was detected in the three RUTI strains. The TEM micrographs showed the presence of short and thin fimbriae only in the UTI-2_245U strain. Conclusion The high variability and genetic diversity of the RUTI strains indicate that are a mosaic of virulence, resistance, and fitness genes that could promote recurrence in susceptible patients.
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Affiliation(s)
- Marco A. Flores-Oropeza
- Posgrado en Ciencias Biomédicas, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Sara A. Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Eva Martínez-Peñafiel
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Rembao-Bojórquez
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Sergio Zavala-Vega
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
- Laboratorio Clínico y Banco de Sangre, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Rigoberto Hernández-Castro
- Departmento de Ecología de Agentes Patógenos, Hospital General “Dr. Manuel Gea González”, Mexico City, Mexico
| | - Marcos Flores-Encarnacion
- Laboratorio de Microbiología Molecular y Celular, Biomedicina, Facultad de Medicina, BUAP, Puebla, Mexico
| | - José Arellano-Galindo
- Laboratorio de Virología Clínica y Experimental, Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Vélez
- Hospital Militar de Especialidades de la Mujer y Neonatología, Mexico City, Mexico
- Unidad Médica de Alta Especialidad, Hospital de Ginecología y Obstetricia No. 3 IMSS, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Putman TE, Schaper K, Matentzoglu N, Rubinetti V, Alquaddoomi F, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese J, Braun I, Bruskiewich R, Cappelletti L, Carbon S, Caron A, Chan L, Chute C, Cortes K, De Souza V, Fontana T, Harris N, Hartley E, Hurwitz E, Jacobsen JB, Krishnamurthy M, Laraway B, McLaughlin J, McMurry J, Moxon ST, Mullen K, O’Neil S, Shefchek K, Stefancsik R, Toro S, Vasilevsky N, Walls R, Whetzel P, Osumi-Sutherland D, Smedley D, Robinson P, Mungall C, Haendel M, Munoz-Torres M. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Res 2024; 52:D938-D949. [PMID: 38000386 PMCID: PMC10767791 DOI: 10.1093/nar/gkad1082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/21/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.
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Affiliation(s)
- Tim E Putman
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kevin Schaper
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Vincent P Rubinetti
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Faisal S Alquaddoomi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Corey Cox
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - J Harry Caufield
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Glass Elsarboukh
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sarah Gehrke
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Harshad Hegde
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Justin T Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian Braun
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | | | | | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anita R Caron
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherina G Cortes
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Tommaso Fontana
- Dipartimento di Informatica, Università degli Studi di Milano Statale, Milano, Italy
| | - Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily L Hartley
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Eric Hurwitz
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Madan Krishnamurthy
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bryan J Laraway
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Julie A McMurry
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sierra A T Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen R Mullen
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Shawn T O’Neil
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kent A Shefchek
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sabrina Toro
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Ramona L Walls
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Patricia L Whetzel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 6032, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Melissa A Haendel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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18
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Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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19
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Bajpai AK, Gu Q, Orgil BO, Alberson NR, Towbin JA, Martinez HR, Lu L, Purevjav E. Exploring the Regulation and Function of Rpl3l in the Development of Early-Onset Dilated Cardiomyopathy and Congestive Heart Failure Using Systems Genetics Approach. Genes (Basel) 2023; 15:53. [PMID: 38254943 PMCID: PMC10815855 DOI: 10.3390/genes15010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cardiomyopathies, diseases affecting the myocardium, are common causes of congestive heart failure (CHF) and sudden cardiac death. Recently, biallelic variants in ribosomal protein L3-like (RPL3L) have been reported to be associated with severe neonatal dilated cardiomyopathy (DCM) and CHF. This study employs a systems genetics approach to gain understanding of the regulatory mechanisms underlying the role of RPL3L in DCM. METHODS Genetic correlation, expression quantitative trait loci (eQTL) mapping, differential expression analysis and comparative functional analysis were performed using cardiac gene expression data from the patients and murine genetic reference populations (GRPs) of BXD mice (recombinant inbred strains from a cross of C57BL/6J and DBA/2J mice). Additionally, immune infiltration analysis was performed to understand the relationship between DCM, immune cells and RPL3L expression. RESULTS Systems genetics analysis identified high expression of Rpl3l mRNA, which ranged from 11.31 to 12.16 across murine GRPs of BXD mice, with an ~1.8-fold difference. Pathways such as "diabetic cardiomyopathy", "focal adhesion", "oxidative phosphorylation" and "DCM" were significantly associated with Rpl3l. eQTL mapping suggested Myl4 (Chr 11) and Sdha (Chr 13) as the upstream regulators of Rpl3l. The mRNA expression of Rpl3l, Myl4 and Sdha was significantly correlated with multiple echocardiography traits in BXD mice. Immune infiltration analysis revealed a significant association of RPL3L and SDHA with seven immune cells (CD4, CD8-naive T cell, CD8 T cell, macrophages, cytotoxic T cell, gamma delta T cell and exhausted T cell) that were also differentially infiltrated between heart samples obtained from DCM patients and normal individuals. CONCLUSIONS RPL3L is highly expressed in the heart tissue of humans and mice. Expression of Rpl3l and its upstream regulators, Myl4 and Sdha, correlate with multiple cardiac function traits in murine GRPs of BXD mice, while RPL3L and SDHA correlate with immune cell infiltration in DCM patient hearts, suggesting important roles for RPL3L in DCM and CHF pathogenesis via immune inflammation, necessitating experimental validations of Myl4 and Sdha in Rpl3l regulation.
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Affiliation(s)
- Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Buyan-Ochir Orgil
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Neely R. Alberson
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Jeffrey A. Towbin
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
- Cardiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hugo R. Martinez
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Enkhsaikhan Purevjav
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
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20
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Dolan M, St. John N, Zaidi F, Doyle F, Fasullo M. High-throughput screening of the Saccharomyces cerevisiae genome for 2-amino-3-methylimidazo [4,5-f] quinoline resistance identifies colon cancer-associated genes. G3 (BETHESDA, MD.) 2023; 13:jkad219. [PMID: 37738679 PMCID: PMC11025384 DOI: 10.1093/g3journal/jkad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/25/2022] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred meats and cigarette smoke. However, few eukaryotic resistance genes have been identified. We used Saccharomyces cerevisiae (budding yeast) to identify genes that confer resistance to 2-amino-3-methylimidazo[4,5-f] quinoline (IQ). CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 µM IQ for 5 or 10 generations. DNA barcodes were sequenced using the Illumina HiSeq 2500 platform and statistical significance was determined for exactly matched barcodes. We identified 424 ORFs, including 337 genes of known function, in duplicate screens of the "humanized" collection for IQ resistance; resistance was further validated for a select group of 51 genes by growth curves, competitive growth, or trypan blue assays. Screens of the library not expressing human genes identified 143 ORFs conferring resistance to IQ per se. Ribosomal protein and protein modification genes were identified as IQ resistance genes in both the original and "humanized" libraries, while nitrogen metabolism, DNA repair, and growth control genes were also prominent in the "humanized" library. Protein complexes identified included the casein kinase 2 (CK2) and histone chaperone (HIR) complex. Among DNA Repair and checkpoint genes, we identified those that function in postreplication repair (RAD18, UBC13, REV7), base excision repair (NTG1), and checkpoint signaling (CHK1, PSY2). These studies underscore the role of ribosomal protein genes in conferring IQ resistance, and illuminate DNA repair pathways for conferring resistance to activated IQ.
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Affiliation(s)
- Michael Dolan
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Nick St. John
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Faizan Zaidi
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Francis Doyle
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Michael Fasullo
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
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21
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Giaccherini M, Gori L, Gentiluomo M, Farinella R, Cervena K, Skieceviciene J, Dijk F, Capurso G, Vezakis A, Archibugi L, Chammas R, Hussein T, Tavano F, Hegyi P, Lovecek M, Izbicki JR, Brenner H, Mohelnikova-Duchonova B, Dell'Anna G, Kupcinskas J, Ermini S, Aoki MN, Neoptolemos JP, Gazouli M, Pasquali C, Pezzilli R, Talar-Wojnarowska R, Oliverius M, Al-Saeedi M, Lucchesi M, Furbetta N, Carrara S, van Eijck CHJ, Maleckas A, Milanetto AC, Lawlor RT, Schöttker B, Boggi U, Morelli L, Ginocchi L, Ponz de Leon Pisani R, Sperti C, Zerbi A, Arcidiacono PG, Uzunoglu FG, Bunduc S, Holleczek B, Gioffreda D, Małecka-Wojciesko E, Kiudelis M, Szentesi A, van Laarhoven HWM, Soucek P, Götz M, Erőss B, Cavestro GM, Basso D, Perri F, Landi S, Canzian F, Campa D. A scan of all coding region variants of the human genome, identifies 13q12.2-rs9579139 and 15q24.1-rs2277598 as novel risk loci for pancreatic ductal adenocarcinoma. Carcinogenesis 2023; 44:642-649. [PMID: 37670727 DOI: 10.1093/carcin/bgad056] [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: 02/16/2023] [Revised: 06/08/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023] Open
Abstract
Coding sequence variants comprise a small fraction of the germline genetic variability of the human genome. However, they often cause deleterious change in protein function and are therefore associated with pathogenic phenotypes. To identify novel pancreatic ductal adenocarcinoma (PDAC) risk loci, we carried out a complete scan of all common missense and synonymous SNPs and analysed them in a case-control study comprising four different populations, for a total of 14 538 PDAC cases and 190 657 controls. We observed a statistically significant association between 13q12.2-rs9581957-T and PDAC risk (P = 2.46 × 10-9), that is in linkage disequilibrium (LD) with a deleterious missense variant (rs9579139) of the URAD gene. Recent findings suggest that this gene is active in peroxisomes. Considering that peroxisomes have a key role as molecular scavengers, especially in eliminating reactive oxygen species, a malfunctioning URAD protein might expose the cell to a higher load of potentially DNA damaging molecules and therefore increase PDAC risk. The association was observed in individuals of European and Asian ethnicity. We also observed the association of the missense variant 15q24.1-rs2277598-T, that belongs to BBS4 gene, with increased PDAC risk (P = 1.53 × 10-6). rs2277598 is associated with body mass index and is in LD with diabetes susceptibility loci. In conclusion, we identified two missense variants associated with the risk of developing PDAC independently from the ethnicity highlighting the importance of conducting reanalysis of genome-wide association studies (GWASs) in light of functional data.
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Affiliation(s)
| | - Leonardo Gori
- Department of Biology, University of Pisa, Pisa, Italy
| | | | | | - Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, Prague, Czech Republic
| | - Jurgita Skieceviciene
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Frederike Dijk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriele Capurso
- Digestive and Liver Disease Unit, S. Andrea Hospital, "Sapienza" University of Rome, Rome, Italy
- Pancreato-Biliary Endoscopy and Endosonography Division, IRCCS San Raffaele Scientific Institute, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, Milan, Italy
| | - Antonis Vezakis
- Department of Surgery, Aretaieio Hospital, Medical School, National and Kapodistrian University of Athens, Athens 11528, Greece
| | - Livia Archibugi
- Digestive and Liver Disease Unit, S. Andrea Hospital, "Sapienza" University of Rome, Rome, Italy
- Pancreato-Biliary Endoscopy and Endosonography Division, IRCCS San Raffaele Scientific Institute, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, Milan, Italy
| | - Roger Chammas
- Departamento de Radiologia e Oncologia, Instituto Do Câncer Do Estado de São Paulo (ICESP), Center for Translational Research in Oncology (LIM24), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil
| | - Tamás Hussein
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Péter Hegyi
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc, Olomouc, Czech Republic
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beatrice Mohelnikova-Duchonova
- Department of Oncology and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital, Olomouc, Czech
| | - Giuseppe Dell'Anna
- Pancreatico/Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Juozas Kupcinskas
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Stefano Ermini
- Blood Transfusion Service, Azienda Ospedaliero-Universitaria Meyer, Children's Hospital, Florence, Italy
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Brazil
| | - John P Neoptolemos
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Claudio Pasquali
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | | | | | - Martin Oliverius
- Department of Surgery, University Hospital Kralovske Vinohrady, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Mohammed Al-Saeedi
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Maurizio Lucchesi
- Department of Medical Oncology, Oncology of Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Niccolò Furbetta
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Silvia Carrara
- Endoscopic Unit, Department of Gastroenterology, IRCCS Humanitas Research, Milan, Italy
| | - Casper H J van Eijck
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Almantas Maleckas
- Department of Surgery, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Anna Caterina Milanetto
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | - Rita T Lawlor
- ARC-Net Centre for Applied Research on Cancer and Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Laura Ginocchi
- Department of Medical Oncology, Oncology of Massa Carrara, Azienda USL Toscana Nord Ovest, Carrara, Italy
| | - Ruggero Ponz de Leon Pisani
- Pancreatico/Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Cosimo Sperti
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | - Alessandro Zerbi
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Paolo Giorgio Arcidiacono
- Pancreatico/Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, San Raffaele Scientific Institute, Milan, Italy
| | - Faik G Uzunoglu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefania Bunduc
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Center for Gastroenterology, Hepatology and Liver Transplant, Fundeni Clinical Institute, Bucharest, Romania
| | | | - Domenica Gioffreda
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | | | - Mindaugas Kiudelis
- Department of Surgery, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
- Department of Medicine, Centre for Translational Medicine, University of Szeged, Szeged, Hungary
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Mara Götz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bálint Erőss
- Center for Translational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Diseases, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Giulia Martina Cavestro
- Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Daniela Basso
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padua, Italy
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
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22
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Wan X, Xiao J, Tam SST, Cai M, Sugimura R, Wang Y, Wan X, Lin Z, Wu AR, Yang C. Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope. Nat Commun 2023; 14:7848. [PMID: 38030617 PMCID: PMC10687049 DOI: 10.1038/s41467-023-43629-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our understanding of tissue spatial architecture and biology. Although current ST methods, whether based on next-generation sequencing (seq-based approaches) or fluorescence in situ hybridization (image-based approaches), offer valuable insights, they face limitations either in cellular resolution or transcriptome-wide profiling. To address these limitations, we present SpatialScope, a unified approach integrating scRNA-seq reference data and ST data using deep generative models. With innovation in model and algorithm designs, SpatialScope not only enhances seq-based ST data to achieve single-cell resolution, but also accurately infers transcriptome-wide expression levels for image-based ST data. We demonstrate SpatialScope's utility through simulation studies and real data analysis from both seq-based and image-based ST approaches. SpatialScope provides spatial characterization of tissue structures at transcriptome-wide single-cell resolution, facilitating downstream analysis, including detecting cellular communication through ligand-receptor interactions, localizing cellular subtypes, and identifying spatially differentially expressed genes.
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Affiliation(s)
- Xiaomeng Wan
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jiashun Xiao
- Shenzhen Research Institute of Big Data, Shenzhen, 518172, China
| | - Sindy Sing Ting Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Mingxuan Cai
- Department of Biostatistics, City University of Hong Kong, Hong Kong SAR, China
| | - Ryohichi Sugimura
- Li Ka Shing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Yang Wang
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Data-Driven Fluid Mechanics and Engineering Applications, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Big Data Bio-Intelligence Lab, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Xiang Wan
- Shenzhen Research Institute of Big Data, Shenzhen, 518172, China
| | - Zhixiang Lin
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Angela Ruohao Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- Center for Aging Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Can Yang
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- Guangdong-Hong Kong-Macao Joint Laboratory for Data-Driven Fluid Mechanics and Engineering Applications, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- Big Data Bio-Intelligence Lab, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
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23
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Allayee H, Farber CR, Seldin MM, Williams EG, James DE, Lusis AJ. Systems genetics approaches for understanding complex traits with relevance for human disease. eLife 2023; 12:e91004. [PMID: 37962168 PMCID: PMC10645424 DOI: 10.7554/elife.91004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.
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Affiliation(s)
- Hooman Allayee
- Departments of Population & Public Health Sciences, University of Southern CaliforniaLos AngelesUnited States
- Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Departments of Biochemistry & Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Public Health Sciences, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
| | - Evan Graehl Williams
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgLuxembourgLuxembourg
| | - David E James
- School of Life and Environmental Sciences, University of SydneyCamperdownAustralia
- Faculty of Medicine and Health, University of SydneyCamperdownAustralia
- Charles Perkins Centre, University of SydneyCamperdownAustralia
| | - Aldons J Lusis
- Departments of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Medicine, University of California, Los AngelesLos AngelesUnited States
- Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLALos AngelesUnited States
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24
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Alnassar N, Hillman C, Fontana BD, Robson SC, Norton WHJ, Parker MO. angptl4 gene expression as a marker of adaptive homeostatic response to social isolation across the lifespan in zebrafish. Neurobiol Aging 2023; 131:209-221. [PMID: 37690345 DOI: 10.1016/j.neurobiolaging.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
Social isolation has detrimental health effects, but the underlying mechanisms are unclear. Here, we investigated the impact of 2 weeks of isolation on behavior and gene expression in the central nervous system at different life stages of zebrafish. Results showed that socially deprived young adult zebrafish experienced increased anxiety, accompanied by changes in gene expression. Most gene expression patterns returned to normal within 24 hours of reintroduction to a social environment, except angptl4, which was upregulated after reintroduction, suggesting an adaptive mechanism. Similarly, aging zebrafish displayed heightened anxiety and increased central nervous system expression of angptl4 during isolation, but effects were reversed upon reintroduction to a social group. The findings imply that angptl4 plays a homeostatic role in response to social isolation, which varies across the lifespan. The study emphasizes the importance of social interactions for psychological well-being and highlights the negative consequences of isolation, especially in older individuals. Further research may unravel how social isolation affects angptl4 expression and its developmental and aging effects.
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Affiliation(s)
- Nancy Alnassar
- School of Pharmacy and Biomedical Science, University of Portsmouth, Portsmouth, UK
| | - Courtney Hillman
- Surrey Sleep Research Centre, University of Surrey, Guilford, UK
| | | | - Samuel C Robson
- School of Pharmacy and Biomedical Science, University of Portsmouth, Portsmouth, UK; School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - William H J Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Matthew O Parker
- Surrey Sleep Research Centre, University of Surrey, Guilford, UK.
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25
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Bornstein K, Gryan G, Chang ES, Marchler-Bauer A, Schneider VA. The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health. BMC Genomics 2023; 24:575. [PMID: 37759191 PMCID: PMC10523801 DOI: 10.1186/s12864-023-09643-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Comparative genomics is the comparison of genetic information within and across organisms to understand the evolution, structure, and function of genes, proteins, and non-coding regions (Sivashankari and Shanmughavel, Bioinformation 1:376-8, 2007). Advances in sequencing technology and assembly algorithms have resulted in the ability to sequence large genomes and provided a wealth of data that are being used in comparative genomic analyses. Comparative analysis can be leveraged to systematically explore and evaluate the biological relationships and evolution between species, aid in understanding the structure and function of genes, and gain a better understanding of disease and potential drug targets. As our knowledge of genetics expands, comparative genomics can help identify emerging model organisms among a broader span of the tree of life, positively impacting human health. This impact includes, but is not limited to, zoonotic disease research, therapeutics development, microbiome research, xenotransplantation, oncology, and toxicology. Despite advancements in comparative genomics, new challenges have arisen around the quantity, quality assurance, annotation, and interoperability of genomic data and metadata. New tools and approaches are required to meet these challenges and fulfill the needs of researchers. This paper focuses on how the National Institutes of Health (NIH) Comparative Genomics Resource (CGR) can address both the opportunities for comparative genomics to further impact human health and confront an increasingly complex set of challenges facing researchers.
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Affiliation(s)
| | - Gary Gryan
- The MITRE Corporation, 7525 Colshire Dr, McLean, VA, USA
| | - E Sally Chang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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26
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Pavone P, Falsaperla R, Ruggieri M, Marino SD, Parano E, Pappalardo XG. A Young Boy with 21q21.1 Microdeletion Showing Speech Delay, Spastic Diplegia, and MRI Abnormalities: Original Case Report. Glob Med Genet 2023; 10:234-239. [PMID: 37663643 PMCID: PMC10471428 DOI: 10.1055/s-0043-1774291] [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: 09/05/2023] Open
Abstract
Chromosome 21q deletion syndrome is a rare disorder affecting the long arm of chromosome 21 and manifesting with wide phenotypic features depending on the size and position of the deleted region. In the syndrome, three distinct deleted regions have been distinguished: region 1, from the centromere to approximately 31.2 Mb (21q11.2-q22.11); region 2, from 31.2 to 36 Mb (21q22.11-q22.12); and region 3, from 36 to 37.5 Mb to the telomere (21q22.12-q22.3). The clinical features are highly variable manifesting with mild, poorly recognizable signs or with severe symptoms including craniofacial dysmorphism, growth failure, developmental delay, behavioral/affective abnormalities, and systemic malformations. We report here the case of a young boy with speech delay, mild spastic diplegia, and brain anomalies on magnetic resonance imaging (MRI). The genetic analysis displayed a microdeletion of the long arm of chromosome 21 approximately extending up to 1.08 Mb. Clinical presentation of the patient and cases of 21q21 deletion reported by the literature are discussed.
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Affiliation(s)
- Piero Pavone
- Department of Child and Experimental Medicine, Section of Paediatrics and Child Neuropsychiatry, University of Catania, Italy
- National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital Policlinico “G. Rodolico-San Marco,” Catania, Italy
- Neonatal Intensive Care Unit, San Marco Hospital, University Hospital Policlinico “G. Rodolico-San Marco,” Catania, Italy
| | - Martino Ruggieri
- Department of Child and Experimental Medicine, Section of Paediatrics and Child Neuropsychiatry, University of Catania, Italy
| | - Simona Domenica Marino
- Neonatal Intensive Care Unit, San Marco Hospital, University Hospital Policlinico “G. Rodolico-San Marco,” Catania, Italy
| | - Enrico Parano
- National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, Italy
| | - Xena Giada Pappalardo
- National Council of Research, Institute for Biomedical Research and Innovation (IRIB), Unit of Catania, Italy
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27
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Wen J, Yi L, Wan L, Dong X. Prognostic value of GLCE and infiltrating immune cells in Ewing sarcoma. Heliyon 2023; 9:e19357. [PMID: 37662777 PMCID: PMC10474439 DOI: 10.1016/j.heliyon.2023.e19357] [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: 02/26/2023] [Revised: 08/10/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023] Open
Abstract
Background The prognostic value of D-glucuronyl C5-epimerase (GLCE) and mast cell infiltration in Ewing sarcoma (ES) has not been well specified and highlighted, which may facilitate survival prediction and treatment. Methods Several qualified datasets were downloaded from the GEO website. Common differentially expressed genes between normal subjects and ES patients in GSE17679, GSE45544, and GSE68776 were identified and screened by multiple algorithms to find hub genes with prognostic value. The prognostic value of 64 infiltrating cells was also explored. A prognostic model was established and then validated with GSE63155 and GSE63156. Finally, functional analysis was performed. Results GLCE and mast cell infiltration were screened as two indicators for a prognostic model. The Kaplan‒Meier analysis showed that patients in the low GLCE expression, mast cell infiltration and risk score groups had poorer outcomes than patients in the high GLCE expression, mast cell infiltration and risk score groups, both in the training and validation sets. Scatter plots and heatmaps also indicated the same results. The concordance indices and calibration analyses indicated a high prediction accuracy of the model in the training and validation sets. The time-dependent receiver operating characteristic analyses suggested high sensitivity and specificity of the model, with area under the curve values between 0.76 and 0.98. The decision curve analyses suggested a significantly higher net benefit by the model than the treat-all and treat-none strategies. Functional analyses suggested that glycosaminoglycan biosynthesis-heparan sulfate/heparin, the cell cycle and microRNAs in cancer were upregulated in ES patients. Conclusions GLCE and mast cell infiltration are potential prognostic indicators in ES. GLCE may affect the proliferation, angiogenesis and metastasis of ES by affecting the biosynthesis of heparan sulfate and heparin.
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Affiliation(s)
- Jian Wen
- Medical College of Nanchang University, Nanchang, Jiangxi, 330006, China
- Department of Orthopedics, JXHC Key Laboratory of Digital Orthopedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China
| | - Lijun Yi
- Central Laboratory, Jiangxi Provincial Children's Hospital, Yangming Rd, Nanchang, Jiangxi, 330006, China
| | - Lijia Wan
- Department of Child Healthcare, Hunan Provincial Maternal and Child Health Hospital, Changsha, Hunan, 410008, China
| | - Xieping Dong
- Medical College of Nanchang University, Nanchang, Jiangxi, 330006, China
- Department of Orthopedics, JXHC Key Laboratory of Digital Orthopedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China
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28
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Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Mamm Genome 2023; 34:364-378. [PMID: 37076585 PMCID: PMC10382347 DOI: 10.1007/s00335-023-09992-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/06/2023] [Indexed: 04/21/2023]
Abstract
Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.
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Affiliation(s)
- Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, 27517, USA
| | - Meghan A Balk
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Robyn L Ball
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | - Anita R Caron
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | | | - Vinicius de Souza
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Sarah Gehrke
- Anschutz Medical Campus, University of Colorado, Aurora, CO, 80045, USA
| | - Melissa Haendel
- Anschutz Medical Campus, University of Colorado, Aurora, CO, 80045, USA
| | - Laura W Harris
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Nomi L Harris
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Arwa Ibrahim
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | | | | | - Julie A McMurry
- Anschutz Medical Campus, University of Colorado, Aurora, CO, 80045, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Tim Putman
- Anschutz Medical Campus, University of Colorado, Aurora, CO, 80045, USA
| | | | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Elliot Sollis
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Anne E Thessen
- Anschutz Medical Campus, University of Colorado, Aurora, CO, 80045, USA
| | - Nicole Vasilevsky
- Data Collaboration Center, Critical Path Institute, Tucson, AZ, 85718, USA
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29
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Nedvědová Š, De Stefano D, Walker O, Hologne M, Miele AE. Revisiting Schistosoma mansoni Micro-Exon Gene (MEG) Protein Family: A Tour into Conserved Motifs and Annotation. Biomolecules 2023; 13:1275. [PMID: 37759676 PMCID: PMC10526429 DOI: 10.3390/biom13091275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Genome sequencing of the human parasite Schistosoma mansoni revealed an interesting gene superfamily, called micro-exon gene (meg), that encodes secreted MEG proteins. The genes are composed of short exons (3-81 base pairs) regularly interspersed with long introns (up to 5 kbp). This article recollects 35 S. mansoni specific meg genes that are distributed over 7 autosomes and one pair of sex chromosomes and that code for at least 87 verified MEG proteins. We used various bioinformatics tools to produce an optimal alignment and propose a phylogenetic analysis. This work highlighted intriguing conserved patterns/motifs in the sequences of the highly variable MEG proteins. Based on the analyses, we were able to classify the verified MEG proteins into two subfamilies and to hypothesize their duplication and colonization of all the chromosomes. Together with motif identification, we also proposed to revisit MEGs' common names and annotation in order to avoid duplication, to help the reproducibility of research results and to avoid possible misunderstandings.
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Affiliation(s)
- Štěpánka Nedvědová
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Chemistry, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 16500 Prague, Czech Republic
- Department of Zoology and Fisheries, Center of Infectious Animal Diseases, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Davide De Stefano
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Olivier Walker
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Maggy Hologne
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
| | - Adriana Erica Miele
- UMR 5280 Institute of Analytical Sciences, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France; (Š.N.); (O.W.); (M.H.)
- Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
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Chodkowski M, Zielezinski A, Anbalagan S. A ligand-receptor interactome atlas of the zebrafish. iScience 2023; 26:107309. [PMID: 37539027 PMCID: PMC10393773 DOI: 10.1016/j.isci.2023.107309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/25/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Studies in zebrafish can unravel the functions of cellular communication and thus identify novel bench-to-bedside drugs targeting cellular communication signaling molecules. Due to the incomplete annotation of zebrafish proteome, the knowledge of zebrafish receptors, ligands, and tools to explore their interactome is limited. To address this gap, we de novo predicted the cellular localization of zebrafish reference proteome using deep learning algorithm. We combined the predicted and existing annotations on cellular localization of zebrafish proteins and created repositories of zebrafish ligands, membrane receptome, and interactome as well as associated diseases and targeting drugs. Unlike other tools, our interactome atlas is based on both the physical interaction data of zebrafish proteome and existing human ligand-receptor pair databases. The resources are available as R and Python scripts. DanioTalk provides a novel resource for researchers interested in targeting cellular communication in zebrafish, as we demonstrate in applications studying synapse and axo-glial interactome. DanioTalk methodology can be applied to build and explore the ligand-receptor atlas of other non-mammalian model organisms.
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Affiliation(s)
- Milosz Chodkowski
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Andrzej Zielezinski
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Savani Anbalagan
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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31
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Hieter P, Andrews B, Fowler D, Bellen H. Highlighting rare disease research with a GENETICS and G3 series on genetic models of rare diseases. Genetics 2023; 224:iyad121. [PMID: 37556311 PMCID: PMC10411596 DOI: 10.1093/genetics/iyad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] Open
Affiliation(s)
- Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Brenda Andrews
- The Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Douglas Fowler
- Department of Genome Sciences and Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Hugo Bellen
- Departments of Molecular and Human Genetics, and Neuroscience Neurological Research Institute, Texas Children's Hospital Baylor College of Medicine, Houston, TX, USA
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32
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Hieter P, Andrews B, Fowler D, Bellen H. Highlighting rare disease research with a GENETICS and G3 series on genetic models of rare diseases. G3 (BETHESDA, MD.) 2023; 13:jkad144. [PMID: 37556359 PMCID: PMC10411584 DOI: 10.1093/g3journal/jkad144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Affiliation(s)
- Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Brenda Andrews
- The Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Douglas Fowler
- Department of Genome Sciences and Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Hugo Bellen
- Departments of Molecular and Human Genetics, and Neuroscience Neurological Research Institute, Texas Children's Hospital Baylor College of Medicine, Houston, TX, USA
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Tan CH, Cheng KW, Park H, Chou TF, Sternberg PW. LINKIN-associated proteins necessary for tissue integrity during collective cell migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527750. [PMID: 36798316 PMCID: PMC9934607 DOI: 10.1101/2023.02.08.527750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell adhesion plays essential roles in almost every aspect of metazoan biology. LINKIN (Human: ITFG1, Caenorhabditis elegans: lnkn-1) is a conserved transmembrane protein that has been identified to be necessary for tissue integrity during migration. In C. elegans, loss of lnkn-1 results in the detachment of the lead migratory cell from the rest of the developing male gonad. Previously, three interactors of ITFG1/lnkn-1 - RUVBL1/ruvb-1, RUVBL2/ruvb-2, and alpha-tubulin - were identified by immunoprecipitation-mass spectrometry (IP-MS) analysis using human HEK293T cells and then validated in the nematode male gonad. The ITFG1-RUVBL1 interaction has since been independently validated in a breast cancer cell line model that also implicates the involvement of the pair in metastasis. Here, we showed that epitope-tagged ITFG1 localized to the cell surface of MDA-MB-231 breast cancer cells. Using IP-MS analysis, we identified a new list of potential interactors of ITFG1. Loss-of-function analysis of their C. elegans orthologs found that three of the interactors - ATP9A/tat-5, NME1/ndk-1, and ANAPC2/apc-2 - displayed migratory detachment phenotypes similar to that of lnkn-1. Taken together with the other genes whose reduction-of-function phenotype is similar to that of lnkn-1 (notably cohesion and condensin), suggests the involvement of membrane remodeling and chromosome biology in LINKIN-dependent cell adhesion and supports the hypothesis for a structural role of chromosomes in post-mitotic cells.
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Affiliation(s)
- Chieh-Hsiang Tan
- Division of Biology and Biological Engineering, California Institute of Technology
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology
| | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology
| | - Paul W. Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology
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Babu V, Bahari R, Laban N, Kulaga J, Abdul Z, Zakkar B, Al-Najjar A, Lesus J, Al-Rifai AAR, Sattar H, Irukulla S, Gunniya P, Requena T, Lysakowski A. RotaRod and acoustic startle reflex performance of two potential mouse models for Meniere's disease. Eur J Neurosci 2023; 58:2708-2723. [PMID: 37461313 DOI: 10.1111/ejn.16083] [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: 01/26/2023] [Revised: 06/11/2023] [Accepted: 06/17/2023] [Indexed: 08/04/2023]
Abstract
Meniere's disease (MD) is a disorder of the inner ear characterized by chronic episodes of vertigo, tinnitus, increased aural pressure, and sensorineural hearing loss. Causes of MD are unknown, but endolymphatic hydrops is a hallmark. In addition, 5%-15% of MD cases have been identified as familial. Whole-genome sequencing studies of individuals with familial MD identified DTNA and FAM136A as candidate genes for autosomal dominant inheritance of MD. Although the exact roles of these genes in MD are unknown, FAM136A encodes a mitochondrial protein, and DTNA encodes a cytoskeletal protein involved in synapse formation and maintenance, important for maintaining the blood-brain barrier. It is also associated with a particular aquaporin. We tested vestibular and auditory function in dtna and fam136a knockout (KO) mice, using RotaRod and startle reflex-based clicker tests, respectively. Three-factor analysis of variance (ANOVA) results indicated that sex, age, and genotype were significantly correlated with reduced mean latencies to fall ("latencies") for male dtna KO mice, while only age was a significant factor for fam136a KO mice. Fam136a KO mice lost their hearing months before WTs (9-11 months vs. 15-20 months). In male dtna KO mice, divergence in mean latencies compared with other genotypes was first evident at 4 months of age, with older males having an even greater decrease. Our results indicate that fam136a gene mutations generate hearing problems, while dtna gene mutations produce balance deficits. Both mouse models should help to elucidate hearing loss and balance-related symptoms associated with MD.
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Affiliation(s)
- Vidya Babu
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Rose Bahari
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Nora Laban
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Jacob Kulaga
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Zahid Abdul
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Basil Zakkar
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Ahmad Al-Najjar
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Joseph Lesus
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | | | - Heba Sattar
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Suhitha Irukulla
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Pranav Gunniya
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Teresa Requena
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Anna Lysakowski
- University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
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Ascencio G, de Cruz MA, Abuel J, Alvarado S, Arriaga Y, Conrad E, Castro A, Eichelberger K, Galvan L, Gundy G, Garcia JAI, Jimenez A, Lu NT, Lugar C, Marania R, Mendsaikhan T, Ortega J, Nand N, Rodrigues NS, Shabazz K, Tam C, Valenciano E, Hayzelden C, Eritano AS, Riggs B. A deficiency screen of the 3rd chromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal. G3 (BETHESDA, MD.) 2023; 13:jkad059. [PMID: 36932646 PMCID: PMC10320142 DOI: 10.1093/g3journal/jkad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023]
Abstract
The mechanism surrounding chromosome inheritance during cell division has been well documented, however, organelle inheritance during mitosis is less understood. Recently, the endoplasmic reticulum (ER) has been shown to reorganize during mitosis, dividing asymmetrically in proneuronal cells prior to cell fate selection, indicating a programmed mechanism of inheritance. ER asymmetric partitioning in proneural cells relies on the highly conserved ER integral membrane protein, Jagunal (Jagn). Knockdown of Jagn in the compound Drosophila eye displays a pleotropic rough eye phenotype in 48% of the progeny. To identify genes involved in Jagn dependent ER partitioning pathway, we performed a dominant modifier screen of the 3rd chromosome for enhancers and suppressors of this Jagn-RNAi-induced rough eye phenotype. We screened through 181 deficiency lines covering the 3L and 3R chromosomes and identified 12 suppressors and 10 enhancers of the Jagn-RNAi phenotype. Based on the functions of the genes covered by the deficiencies, we identified genes that displayed a suppression or enhancement of the Jagn-RNAi phenotype. These include Division Abnormally Delayed (Dally), a heparan sulfate proteoglycan, the γ-secretase subunit Presenilin, and the ER resident protein Sec63. Based on our understanding of the function of these targets, there is a connection between Jagn and the Notch signaling pathway. Further studies will elucidate the role of Jagn and identified interactors within the mechanisms of ER partitioning during mitosis.
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Affiliation(s)
- Gerson Ascencio
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Matthew A de Cruz
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Judy Abuel
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Sydney Alvarado
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Yuma Arriaga
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Emily Conrad
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Alonso Castro
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Katharine Eichelberger
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Laura Galvan
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Grace Gundy
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | | | - Alyssa Jimenez
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Nhien Tuyet Lu
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Catharine Lugar
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Ronald Marania
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Tserendavaa Mendsaikhan
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Jose Ortega
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Natasha Nand
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Nicole S Rodrigues
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Khayla Shabazz
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Cynnie Tam
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Emmanuel Valenciano
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Clive Hayzelden
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Anthony S Eritano
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
| | - Blake Riggs
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 4132, USA
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36
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Hu Y, Comjean A, Attrill H, Antonazzo G, Thurmond J, Chen W, Li F, Chao T, Mohr SE, Brown NH, Perrimon N. PANGEA: a new gene set enrichment tool for Drosophila and common research organisms. Nucleic Acids Res 2023; 51:W419-W426. [PMID: 37125646 PMCID: PMC10320058 DOI: 10.1093/nar/gkad331] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/28/2023] [Accepted: 04/29/2023] [Indexed: 05/02/2023] Open
Abstract
Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualizations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.
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Affiliation(s)
- Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Weihang Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Fangge Li
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tiffany Chao
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Nicholas H Brown
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02138, USA
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37
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Huang X, Bajpai AK, Sun J, Xu F, Lu L, Yousefi S. A new gene-scoring method for uncovering novel glaucoma-related genes using non-negative matrix factorization based on RNA-seq data. Front Genet 2023; 14:1204909. [PMID: 37377596 PMCID: PMC10292752 DOI: 10.3389/fgene.2023.1204909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Early diagnosis and treatment of glaucoma are challenging. The discovery of glaucoma biomarkers based on gene expression data could potentially provide new insights for early diagnosis, monitoring, and treatment options of glaucoma. Non-negative Matrix Factorization (NMF) has been widely used in numerous transcriptome data analyses in order to identify subtypes and biomarkers of different diseases; however, its application in glaucoma biomarker discovery has not been previously reported. Our study applied NMF to extract latent representations of RNA-seq data from BXD mouse strains and sorted the genes based on a novel gene scoring method. The enrichment ratio of the glaucoma-reference genes, extracted from multiple relevant resources, was compared using both the classical differentially expressed gene (DEG) analysis and NMF methods. The complete pipeline was validated using an independent RNA-seq dataset. Findings showed our NMF method significantly improved the enrichment detection of glaucoma genes. The application of NMF with the scoring method showed great promise in the identification of marker genes for glaucoma.
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Affiliation(s)
- Xiaoqin Huang
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Akhilesh K. Bajpai
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jian Sun
- Integrated Data Science Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institute of Health (NIH), Bethesda, MD, United States
| | - Fuyi Xu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Lu Lu
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Siamak Yousefi
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, United States
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
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38
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Turco G, Chang C, Wang RY, Kim G, Stoops EH, Richardson B, Sochat V, Rust J, Oughtred R, Thayer N, Kang F, Livstone MS, Heinicke S, Schroeder M, Dolinski KJ, Botstein D, Baryshnikova A. Global analysis of the yeast knockout phenome. SCIENCE ADVANCES 2023; 9:eadg5702. [PMID: 37235661 PMCID: PMC11326039 DOI: 10.1126/sciadv.adg5702] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae, enabled by its knockout collection, have produced the largest, richest, and most systematic phenotypic description of any organism. However, integrative analyses of this rich data source have been virtually impossible because of the lack of a central data repository and consistent metadata annotations. Here, we describe the aggregation, harmonization, and analysis of ~14,500 yeast knockout screens, which we call Yeast Phenome. Using this unique dataset, we characterized two unknown genes (YHR045W and YGL117W) and showed that tryptophan starvation is a by-product of many chemical treatments. Furthermore, we uncovered an exponential relationship between phenotypic similarity and intergenic distance, which suggests that gene positions in both yeast and human genomes are optimized for function.
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Affiliation(s)
- Gina Turco
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Christie Chang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Griffin Kim
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Brianna Richardson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Vanessa Sochat
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Rust
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Rose Oughtred
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Fan Kang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael S Livstone
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sven Heinicke
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mark Schroeder
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kara J Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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39
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Kalotay E, Klugmann M, Housley GD, Fröhlich D. Recessive aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models. Front Neurosci 2023; 17:1182874. [PMID: 37274208 PMCID: PMC10234152 DOI: 10.3389/fnins.2023.1182874] [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: 03/09/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Protein synthesis is a fundamental process that underpins almost every aspect of cellular functioning. Intriguingly, despite their common function, recessive mutations in aminoacyl-tRNA synthetases (ARSs), the family of enzymes that pair tRNA molecules with amino acids prior to translation on the ribosome, cause a diverse range of multi-system disorders that affect specific groups of tissues. Neurological development is impaired in most ARS-associated disorders. In addition to central nervous system defects, diseases caused by recessive mutations in cytosolic ARSs commonly affect the liver and lungs. Patients with biallelic mutations in mitochondrial ARSs often present with encephalopathies, with variable involvement of peripheral systems. Many of these disorders cause severe disability, and as understanding of their pathogenesis is currently limited, there are no effective treatments available. To address this, accurate in vivo models for most of the recessive ARS diseases are urgently needed. Here, we discuss approaches that have been taken to model recessive ARS diseases in vivo, highlighting some of the challenges that have arisen in this process, as well as key results obtained from these models. Further development and refinement of animal models is essential to facilitate a better understanding of the pathophysiology underlying recessive ARS diseases, and ultimately to enable development and testing of effective therapies.
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Affiliation(s)
- Elizabeth Kalotay
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthias Klugmann
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gary D. Housley
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Dominik Fröhlich
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
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Wong ED, Miyasato SR, Aleksander S, Karra K, Nash RS, Skrzypek MS, Weng S, Engel SR, Cherry JM. Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources. Genetics 2023; 224:iyac191. [PMID: 36607068 PMCID: PMC10158836 DOI: 10.1093/genetics/iyac191] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/16/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architecture, to curation of novel data types, to incorporation of data from, and collaboration with, other knowledgebases. We are continuing to make steps toward providing the community with an S. cerevisiae pan-genome. Here, we describe software upgrades, a new nomenclature system for genes not found in the reference strain, and additions to gene pages. With these improvements, we aim to remain a leading resource for students, researchers, and the broader scientific community.
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Affiliation(s)
- Edith D Wong
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Suzi Aleksander
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Robert S Nash
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Marek S Skrzypek
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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Bradford YM, Van Slyke CE, Howe DG, Fashena D, Frazer K, Martin R, Paddock H, Pich C, Ramachandran S, Ruzicka L, Singer A, Taylor R, Tseng WC, Westerfield M. From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes. Genetics 2023; 224:iyad032. [PMID: 36864549 PMCID: PMC10158835 DOI: 10.1093/genetics/iyad032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Danio rerio is a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for genetic, genomic, and phenotypic data that result from research using D. rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.
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Affiliation(s)
- Yvonne M Bradford
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ceri E Van Slyke
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Douglas G Howe
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - David Fashena
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ken Frazer
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ryan Martin
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Holly Paddock
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Christian Pich
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | | | - Leyla Ruzicka
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Amy Singer
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Ryan Taylor
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Wei-Chia Tseng
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
| | - Monte Westerfield
- The Institute of Neuroscience, University of Oregon, Eugene, OR 97403-1254, USA
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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: 389] [Impact Index Per Article: 389.0] [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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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: 14] [Impact Index Per Article: 14.0] [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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Hu Y, Comjean A, Attrill H, Antonazzo G, Thurmond J, Li F, Chao T, Mohr SE, Brown NH, Perrimon N. PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529262. [PMID: 36865134 PMCID: PMC9980003 DOI: 10.1101/2023.02.20.529262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/ ), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualisations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.
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Affiliation(s)
- Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Aram Comjean
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Fangge Li
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tiffany Chao
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stephanie E. Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Nicholas H. Brown
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02138, USA
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Carli ALE, Hardy JM, Hoblos H, Ernst M, Lucet IS, Buchert M. Structure-Guided Prediction of the Functional Impact of DCLK1 Mutations on Tumorigenesis. Biomedicines 2023; 11:biomedicines11030990. [PMID: 36979969 PMCID: PMC10046695 DOI: 10.3390/biomedicines11030990] [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: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Doublecortin-like kinase 1 (DCLK1) is a functional serine/threonine (S/T)-kinase and a member of the doublecortin family of proteins which are characterized by their ability to bind to microtubules (MTs). DCLK1 is a proposed cancer driver gene, and its upregulation is associated with poor overall survival in several solid cancer types. However, how DCLK1 associates with MTs and how its kinase function contributes to pro-tumorigenic processes is poorly understood. This review builds on structural models to propose not only the specific functions of the domains but also attempts to predict the impact of individual somatic missense mutations on DCLK1 functions. Somatic missense mutations in DCLK1 are most frequently located within the N-terminal MT binding region and likely impact on the ability of DCLK1 to bind to αβ-tubulin and to polymerize and stabilize MTs. Moreover, the MT binding affinity of DCLK1 is negatively regulated by its auto-phosphorylation, and therefore mutations that affect kinase activity are predicted to indirectly alter MT dynamics. The emerging picture portrays DCLK1 as an MT-associated protein whose interactions with tubulin heterodimers and MTs are tightly controlled processes which, when disrupted, may confer pro-tumorigenic properties.
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Affiliation(s)
- Annalisa L E Carli
- Cancer Inflammation Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Joshua M Hardy
- ACRF Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Hanadi Hoblos
- ACRF Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthias Ernst
- Cancer Inflammation Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - Isabelle S Lucet
- ACRF Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael Buchert
- Cancer Inflammation Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
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Liu C, Wang XL, Shen EC, Wang BZ, Meng R, Cui Y, Wang WJ, Shao Q. Bioinformatics analysis of prognosis and immune microenvironment of immunological cell death-related gemcitabine-resistance genes in bladder cancer. Transl Androl Urol 2022; 11:1715-1728. [PMID: 36632166 PMCID: PMC9827393 DOI: 10.21037/tau-22-736] [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: 10/12/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Background Bladder cancer (BC) is the most common malignant tumor of the urinary system. Gemcitabine resistance partly accounts for treatment failure and recurrence in BC. Immunological cell death (ICD) is correlated with chemoresistance. The prognosis of patients with similar tumor stage still varies in response to chemotherapy, recurrence, and disease progression. Therefore, our study aimed to provide a prognostic model based on ICD-related and gemcitabine-resistance genes for BC. Methods The data of BC patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs), and differentially expressed gemcitabine resistance-related genes (DEGRRGs) were identified using the edgeR package. The survival-associated DEGRRGs were identified by univariate Cox analysis. A prognostic model was established by univariate Cox regression analysis and validated by GEO dataset. The outcome of low-risk group and high-risk group was analyzed by the Kaplan-Meier curve. The relationship between risk score and immune cell infiltration was investigated using the TIMER online database. Results The prognosis of patients in the ICD-high group was significantly better than ICD-low group. A prognostic model containing 5 gemcitabine resistance-related ICD-associated genes, including PTPRR, HOXB3, SIGLEC15, UNC5CL, and CASQ1, was established. In both TCGA prognostic model and GEO validation model, patients in the low-risk group had better outcomes than high-risk group. According to the receiver operating characteristic (ROC) curves, the risk score area under ROC curve (AUC) of the TCGA prognostic model were calculated to be 0.705, while the risk score of the GEO validation model were calculated to be 0.716. Patients in the high-risk group had a significantly higher immune score, stromal score, and infiltration of M0 macrophages, M1 macrophages, M2 macrophages, and activated CD4+ T cells. Patients in the high-risk group had significantly lower infiltration of the regulatory T cells, resting dendritic cell (DCs), and activated DCs. Conclusions The present study highlighted the functional role of gemcitabine resistance-related ICD-associated genes, constructed a prognostic score for the outcome evaluation and searched for potential targets to overcome gemcitabine chemoresistance in BC.
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Affiliation(s)
- Chao Liu
- Department of Urology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xiao-Lan Wang
- Department of Urology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Er-Chang Shen
- Department of Clinical Medicine, Nantong University, Nantong, China
| | - Bing-Zhi Wang
- Department of Urology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Rui Meng
- Department of Urology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yong Cui
- Department of Urology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Wen-Jie Wang
- Department of Radio-Oncology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Qiang Shao
- Department of Urology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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Zhao X, Zhao Y, Jiang Y, Zhang Q. Deciphering the endometrial immune landscape of RIF during the window of implantation from cellular senescence by integrated bioinformatics analysis and machine learning. Front Immunol 2022; 13:952708. [PMID: 36131919 PMCID: PMC9484583 DOI: 10.3389/fimmu.2022.952708] [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: 05/25/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Recurrent implantation failure (RIF) is an extremely thorny issue in in-vitro fertilization (IVF)-embryo transfer (ET). However, its intricate etiology and pathological mechanisms are still unclear. Nowadays, there has been extensive interest in cellular senescence in RIF, and its involvement in endometrial immune characteristics during the window of implantation (WOI) has captured scholars' growing concerns. Therefore, this study aims to probe into the pathological mechanism of RIF from cellular senescence and investigate the correlation between cellular senescence and endometrial immune characteristics during WOI based on bioinformatics combined with machine learning strategy, so as to elucidate the underlying pathological mechanisms of RIF and to explore novel treatment strategies for RIF. Firstly, the gene sets of GSE26787 and GSE111974 from the Gene Expression Omnibus (GEO) database were included for the weighted gene correlation network analysis (WGCNA), from which we concluded that the genes of the core module were closely related to cell fate decision and immune regulation. Subsequently, we identified 25 cellular senescence-associated differentially expressed genes (DEGs) in RIF by intersecting DEGs with cellular senescence-associated genes from the Cell Senescence (CellAge) database. Moreover, functional enrichment analysis was conducted to further reveal the specific molecular mechanisms by which these molecules regulate cellular senescence and immune pathways. Then, eight signature genes were determined by the machine learning method of support vector machine-recursive feature elimination (SVM-RFE), random forest (RF), and artificial neural network (ANN), comprising LATS1, EHF, DUSP16, ADCK5, PATZ1, DEK, MAP2K1, and ETS2, which were also validated in the testing gene set (GSE106602). Furthermore, distinct immune microenvironment abnormalities in the RIF endometrium during WOI were comprehensively explored and validated in GSE106602, including infiltrating immunocytes, immune function, and the expression profiling of human leukocyte antigen (HLA) genes and immune checkpoint genes. Moreover, the correlation between the eight signature genes with the endometrial immune landscape of RIF was also evaluated. After that, two distinct subtypes with significantly distinct immune infiltration characteristics were identified by consensus clustering analysis based on the eight signature genes. Finally, a "KEGG pathway-RIF signature genes-immune landscape" association network was constructed to intuitively uncover their connection. In conclusion, this study demonstrated that cellular senescence might play a pushing role in the pathological mechanism of RIF, which might be closely related to its impact on the immune microenvironment during the WOI phase. The exploration of the molecular mechanism of cellular senescence in RIF is expected to bring new breakthroughs for disease diagnosis and treatment strategies.
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Affiliation(s)
- Xiaoxuan Zhao
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
| | - Yang Zhao
- College of Basic Medicine, Hebei College of Traditional Chinese Medicine, Shijiazhuang, China
| | - Yuepeng Jiang
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qin Zhang
- Department of Traditional Chinese Medicine (TCM) Gynecology, Hangzhou Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Hangzhou, China
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48
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Cheng KC, Burdine RD, Dickinson ME, Ekker SC, Lin AY, Lloyd KCK, Lutz CM, MacRae CA, Morrison JH, O'Connor DH, Postlethwait JH, Rogers CD, Sanchez S, Simpson JH, Talbot WS, Wallace DC, Weimer JM, Bellen HJ. Promoting validation and cross-phylogenetic integration in model organism research. Dis Model Mech 2022; 15:dmm049600. [PMID: 36125045 PMCID: PMC9531892 DOI: 10.1242/dmm.049600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Model organism (MO) research provides a basic understanding of biology and disease due to the evolutionary conservation of the molecular and cellular language of life. MOs have been used to identify and understand the function of orthologous genes, proteins, cells and tissues involved in biological processes, to develop and evaluate techniques and methods, and to perform whole-organism-based chemical screens to test drug efficacy and toxicity. However, a growing richness of datasets and the rising power of computation raise an important question: How do we maximize the value of MOs? In-depth discussions in over 50 virtual presentations organized by the National Institutes of Health across more than 10 weeks yielded important suggestions for improving the rigor, validation, reproducibility and translatability of MO research. The effort clarified challenges and opportunities for developing and integrating tools and resources. Maintenance of critical existing infrastructure and the implementation of suggested improvements will play important roles in maintaining productivity and facilitating the validation of animal models of human biology and disease.
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Affiliation(s)
- Keith C. Cheng
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, Park, PA 16802, USA
| | - Rebecca D. Burdine
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Mary E. Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77007, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77007, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55906, USA
| | - Alex Y. Lin
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - K. C. Kent Lloyd
- Mouse Biology Program, School of Medicinel, University of California Davis, Davis, CA 95618, USA
- Department of Surgery, School of Medicine, University of California Davis, Davis, CA 95618, USA
| | - Cathleen M. Lutz
- The Jackson Laboratory, Genetic Resource Science, Bar Harbor, ME 04609, USA
| | - Calum A. MacRae
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 360 Longwood Avenue, Boston, MA 02215, USA
| | - John H. Morrison
- California National Primate Research Center, University of California Davis, Davis, CA 95616, USA
- Department of Neurology, University of California Davis, Davis, CA 95616, USA
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University ofWisconsin-Madison, Madison, WI 53711, USA
| | | | - Crystal D. Rogers
- School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA 30602, USA
| | - Julie H. Simpson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA 93117, USA
| | - William S. Talbot
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Douglas C. Wallace
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jill M. Weimer
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Neurological Research Institute (TCH), Baylor College of Medicine, Houston, TX 77007, USA
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49
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Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci 2022; 15:1848-1855. [PMID: 36125173 PMCID: PMC9372416 DOI: 10.1111/cts.13302] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these "knowledge graphs" (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open-access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open-source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object-oriented classification and graph-oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.
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Grants
- OT3TR002019 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003445 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003449 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002515 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002584 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003434 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- RM1 HG010860 NHGRI NIH HHS
- OT2TR003433 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003435 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002517 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002027 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003422 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003441 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002020 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3 TR002019 NCATS NIH HHS
- OT2TR003448 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003428 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002520 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003427 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003436 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR002514 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- R24 OD011883 NIH HHS
- OT2TR003443 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002025 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2 TR003428 NCATS NIH HHS
- OT2TR003437 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003450 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT3TR002026 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- OT2TR003430 National Center for Advancing Translational Sciences, Biomedical Data Translator Program
- U.S. Department of Energy
- National Human Genome Research Institute
- National Institutes of Health
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Affiliation(s)
- Deepak R. Unni
- Genome Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
- Division of Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Sierra A. T. Moxon
- Division of Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Michael Bada
- Center for Health AIUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Matthew Brush
- Center for Health AIUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | | | - J. Harry Caufield
- Division of Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Paul A. Clemons
- Chemical Biology and Therapeutics Science ProgramBroad InstituteCambridgeMassachusettsUSA
| | - Vlado Dancik
- Chemical Biology and Therapeutics Science ProgramBroad InstituteCambridgeMassachusettsUSA
| | - Michel Dumontier
- Institute of Data ScienceMaastricht UniversityMaastrichtThe Netherlands
| | - Karamarie Fecho
- Renaissance Computing InstituteUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | | | | | - Nomi L. Harris
- Division of Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Arpita Joshi
- Institute for Systems BiologySeattleWashingtonUSA
| | - Tim Putman
- Center for Health AIUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | | | - Stephen A. Ramsey
- Department of Biomedical SciencesOregon State UniversityCorvallisOregonUSA
| | - Kent A. Shefchek
- Center for Health AIUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | | | - Karthik Soman
- Department of NeurologyUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Anne E. Thessen
- Center for Health AIUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Melissa A. Haendel
- Center for Health AIUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Chris Bizon
- Renaissance Computing InstituteUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Christopher J. Mungall
- Division of Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
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50
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Martinez MAQ, Matus DQ. CDK activity sensors: genetically encoded ratiometric biosensors for live analysis of the cell cycle. Biochem Soc Trans 2022; 50:1081-1090. [PMID: 35674434 PMCID: PMC9661961 DOI: 10.1042/bst20211131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/09/2022] [Accepted: 05/18/2022] [Indexed: 01/04/2023]
Abstract
Cyclin-dependent kinase (CDK) sensors have facilitated investigations of the cell cycle in living cells. These genetically encoded fluorescent biosensors change their subcellular location upon activation of CDKs. Activation is primarily regulated by their association with cyclins, which in turn trigger cell-cycle progression. In the absence of CDK activity, cells exit the cell cycle and become quiescent, a key step in stem cell maintenance and cancer cell dormancy. The evolutionary conservation of CDKs has allowed for the rapid development of CDK activity sensors for cell lines and several research organisms, including nematodes, fish, and flies. CDK activity sensors are utilized for their ability to visualize the exact moment of cell-cycle commitment. This has provided a breakthrough in understanding the proliferation-quiescence decision. Further adoption of these biosensors will usher in new discoveries focused on the cell-cycle regulation of development, ageing, and cancer.
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Affiliation(s)
- Michael A Q Martinez
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, U.S.A
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, U.S.A
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