1
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Haberman N, Cheung R, Pizza G, Cvetesic N, Nagy D, Maude H, Blazquez L, Lenhard B, Cebola I, Rutter GA, Martinez-Sanchez A. Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells. FASEB J 2024; 38:e23885. [PMID: 39139039 PMCID: PMC11378476 DOI: 10.1096/fj.202401078r] [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: 05/13/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination of Lkb1 from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell-selective deletion of Lkb1 on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors (TFs) important for β-cell identity, such as FOXA, MAFA or RFX6, and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.
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Affiliation(s)
- Nejc Haberman
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Rebecca Cheung
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Grazia Pizza
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
| | - Nevena Cvetesic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Dorka Nagy
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Lorea Blazquez
- Department of Neurosciences, Biogipuzkoa Health Research Institute, San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), Madrid, Spain
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Lee Kong Chian Medical School, Nanyang Technological University, Singapore, Singapore
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Faculty of Medicine, Imperial College London, London, UK
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2
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Kruangkum T, Jaiboon K, Pakawanit P, Saetan J, Pudgerd A, Wannapaiboon S, Chotwiwatthanakun C, Cummins SF, Sobhon P, Vanichviriyakit R. Anatomical and molecular insights into the antennal gland of the giant freshwater prawn Macrobrachium rosenbergii. Cell Tissue Res 2024; 397:125-146. [PMID: 38878176 PMCID: PMC11291661 DOI: 10.1007/s00441-024-03898-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 05/07/2024] [Indexed: 08/03/2024]
Abstract
In this study, the complex organization of the AnG in the giant freshwater prawn Macrobrachium rosenbergii was revealed using various techniques, including conventional histology, histochemistry, scanning electron microscopy, and X-ray tomography. The results showed the diversity of cells in the AnG and the detailed organization of the labyrinth's tubule into four radiated areas from the central to peripheral zones. The study also demonstrated the expression of some vertebrate kidney-associated homolog genes, aquaporin (AQP), solute carrier family 22 (SLC-22), nephrin, and uromodulin, in the AnG by qPCR. The result of in situ hybridization further showed the localization of SLC-22 and AQP transcript in the bladder and labyrinth's epithelium, specifically in regions 2, 3, and 4. Additionally, the study revealed neuropeptide expressions in the AnG by qPCR and in situ hybridization, i.e., crustacean hyperglycemic hormone (CHH) and molt inhibiting hormone (MIH), implying that the AnG may have a role in hormone production. Moreover, male and female prawns exhibited different levels of AQP, SLC-22, nephrin, and CHH expressions during the premolt and intermolt stages, suggesting a crucial role relevant to the molting stages. In conclusion, this study clarified the complex structure of the AnG in M. rosenbergii and demonstrated for the first time the expression of vertebrate kidney-associated genes and the possible endocrine role of the AnG. Further investigation is needed to clarify the role of these genes, particularly during ecdysis. The implications of these findings could significantly advance our understanding of the AnG in decapod crustaceans.
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Affiliation(s)
- Thanapong Kruangkum
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Kornchanok Jaiboon
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Phakkhananan Pakawanit
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, 30000, Thailand
| | - Jirawat Saetan
- Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Arnon Pudgerd
- Division of Anatomy, School of Medical Science, University of Phayao, Muang, Phayao, 56000, Thailand
| | - Suttipong Wannapaiboon
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, 30000, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Mahidol University, Nakhonsawan Campus, Nakhonsawan, 60130, Thailand
| | - Scott F Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore DC, Sippy Downs, QLD, 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Sippy Downs, QLD, 4558, Australia
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Rapeepun Vanichviriyakit
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.
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3
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Chandrasekaran V, Wellens S, Bourguignon A, Djidrovski I, Fransen L, Ghosh S, Mazidi Z, Murphy C, Nunes C, Singh P, Zana M, Armstrong L, Dinnyés A, Grillari J, Grillari-Voglauer R, Leonard MO, Verfaillie C, Wilmes A, Zurich MG, Exner T, Jennings P, Culot M. Evaluation of the impact of iPSC differentiation protocols on transcriptomic signatures. Toxicol In Vitro 2024; 98:105826. [PMID: 38615723 DOI: 10.1016/j.tiv.2024.105826] [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: 03/26/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Human induced pluripotent stem cells (iPSC) have the potential to produce desired target cell types in vitro and allow for the high-throughput screening of drugs/chemicals at population level thereby minimising the cost of drug discovery and drug withdrawals after clinical trials. There is a substantial need for the characterisation of the iPSC derived models to better understand and utilise them for toxicological relevant applications. In our study, iPSC (SBAD2 or SBAD3 lines obtained from StemBANCC project) were differentiated towards toxicologically relevant cell types: alveolar macrophages, brain capillary endothelial cells, brain cells, endothelial cells, hepatocytes, lung airway epithelium, monocytes, podocytes and renal proximal tubular cells. A targeted transcriptomic approach was employed to understand the effects of differentiation protocols on these cell types. Pearson correlation and principal component analysis (PCA) separated most of the intended target cell types and undifferentiated iPSC models as distinct groups with a high correlation among replicates from the same model. Based on PCA, the intended target cell types could also be separated into the three germ layer groups (ectoderm, endoderm and mesoderm). Differential expression analysis (DESeq2) presented the upregulated genes in each intended target cell types that allowed the evaluation of the differentiation to certain degree and the selection of key differentiation markers. In conclusion, these data confirm the versatile use of iPSC differentiated cell types as standardizable and relevant model systems for in vitro toxicology.
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Affiliation(s)
- Vidya Chandrasekaran
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Sara Wellens
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France
| | - Aurore Bourguignon
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Ivo Djidrovski
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - Leonie Fransen
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Sreya Ghosh
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Zahra Mazidi
- Evercyte GmbH, Vienna, Austria; Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cormac Murphy
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Carolina Nunes
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | - Pranika Singh
- Edelweiss Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, 4057 Basel, Switzerland; Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | | | - Lyle Armstrong
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, UK
| | - András Dinnyés
- BioTalentum Ltd, Gödöllő, Hungary; Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, H-2100, Gödöllő, Hungary
| | - Johannes Grillari
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Ludwig Boltzmann Institute for Traumatology in cooperation with AUVA, Vienna, Austria
| | | | - Martin O Leonard
- Toxicology Department, Radiation, Chemical and Environmental Hazards (RCE) Directorate, UK Health Security Agency, Harwell Campus, OX11 0RQ, UK
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands
| | - Marie-Gabrielle Zurich
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | | | - Paul Jennings
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081HZ Amsterdam, the Netherlands.
| | - Maxime Culot
- University of Artois, UR 2465, Laboratoire de la Barrière Hémato-Encéphalique (LBHE), Faculté des sciences Jean Perrin, Rue Jean Souvraz SP18, F-62300 Lens, France.
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Haberman N, Cheung R, Pizza G, Cvetesic N, Nagy D, Maude H, Blazquez L, Lenhard B, Cebola I, Rutter GA, Martinez-Sanchez A. Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593867. [PMID: 38798508 PMCID: PMC11118353 DOI: 10.1101/2024.05.13.593867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Liver kinase B1 (LKB1/STK11) is an important regulator of pancreatic β-cell identity and function. Elimination of Lkb1 from the β-cell results in improved glucose-stimulated insulin secretion and is accompanied by profound changes in gene expression, including the upregulation of several neuronal genes. The mechanisms through which LKB1 controls gene expression are, at present, poorly understood. Here, we explore the impact of β cell- selective deletion of Lkb1 on chromatin accessibility in mouse pancreatic islets. To characterize the role of LKB1 in the regulation of gene expression at the transcriptional level, we combine these data with a map of islet active transcription start sites and histone marks. We demonstrate that LKB1 elimination from β-cells results in widespread changes in chromatin accessibility, correlating with changes in transcript levels. Changes occurred in hundreds of promoter and enhancer regions, many of which were close to neuronal genes. We reveal that dysregulated enhancers are enriched in binding motifs for transcription factors important for β-cell identity, such as FOXA, MAFA or RFX6 and we identify microRNAs (miRNAs) that are regulated by LKB1 at the transcriptional level. Overall, our study provides important new insights into the epigenetic mechanisms by which LKB1 regulates β-cell identity and function.
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5
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Rong J, Xie X, Niu Y, Su Z. Correlation between the RNA Expression and the DNA Methylation of Estrogen Receptor Genes in Normal and Malignant Human Tissues. Curr Issues Mol Biol 2024; 46:3610-3625. [PMID: 38666956 PMCID: PMC11049367 DOI: 10.3390/cimb46040226] [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: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Estrogen plays a multifaceted function in humans via interacting with the estrogen receptors ERα, ERβ, and G protein-coupled estrogen receptor 1 (GPER1). Previous research has predominantly concentrated on elucidating the signaling route of estrogen. However, the comprehensive understanding of the expression profile and control of these estrogen receptors in various human tissues is not well known. In the present study, the RNA levels of estrogen receptors in various normal and malignant human tissues were retrieved from the human protein atlas, the cancer genome atlas (TCGA), and the genotype-tissue expression (GTEx) databases for analyzing the expression profile of estrogen receptors through gene expression profiling interactive analysis (GEPIA). The status of DNA methylation of estrogen receptor genes from TCGA were analyzed through the software Wanderer and cBioPortal. The MethSurv tool was utilized to estimate the relevance between specific cytosine-guanine (CG) methylation and tumor survival. The expression profile analysis revealed that ERα, ERβ, and GPER1 have unique expression patterns in diverse tissues and malignancies. The interesting results were the higher expression of ERβ RNA in the male testis than in females and the positive association between the RNA level of ERα and the androgen receptor in different human normal tissues. Especially, the significant changes in GPER1 expression in multiple malignancies showed a consistent decrease with no exception, which indicates the role of GPER1 in common tumor inhibition. The finding on the expression profile provides clues for exploring novel potential physiological and pathophysiological functions of estrogen. The DNA methylation analysis manifested that the expression of GPER1 and ERα showed a substantial correlation with the methylation of specific CG sites in the cis-regulating region of the gene. However, no such association was observed for ERβ. When comparing tumor tissues to normal tissues, the DNA methylation of certain CG sites of estrogen receptors showed a correlation with tumor survival but did not always correlate with the expression of that gene or with the expression of DNA methyltransferases. We proposed that the variation in DNA methylation at different CG sites in estrogen receptor genes had other functions beyond its regulatory role in its gene expression, and this might be associated with the progression and therapy efficiency of the tumor based on the modulation of the chromatin configuration.
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Affiliation(s)
- Ju Rong
- The First Clinical Institute, Shantou University Medical College, Shantou 515041, China
| | - Xiaojun Xie
- Department of Histology and Embryology, Shantou University Medical College, Shantou 515041, China
| | - Yongdong Niu
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
| | - Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, Shantou 515041, China
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6
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Cacho-Navas C, López-Pujante C, Reglero-Real N, Colás-Algora N, Cuervo A, Conesa JJ, Barroso S, de Rivas G, Ciordia S, Paradela A, D'Agostino G, Manzo C, Feito J, Andrés G, Molina-Jiménez F, Majano P, Correas I, Carazo JM, Nourshargh S, Huch M, Millán J. ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin. eLife 2024; 12:RP89261. [PMID: 38597186 PMCID: PMC11006420 DOI: 10.7554/elife.89261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Epithelial intercellular adhesion molecule (ICAM)-1 is apically polarized, interacts with, and guides leukocytes across epithelial barriers. Polarized hepatic epithelia organize their apical membrane domain into bile canaliculi and ducts, which are not accessible to circulating immune cells but that nevertheless confine most of ICAM-1. Here, by analyzing ICAM-1_KO human hepatic cells, liver organoids from ICAM-1_KO mice and rescue-of-function experiments, we show that ICAM-1 regulates epithelial apicobasal polarity in a leukocyte adhesion-independent manner. ICAM-1 signals to an actomyosin network at the base of canalicular microvilli, thereby controlling the dynamics and size of bile canalicular-like structures. We identified the scaffolding protein EBP50/NHERF1/SLC9A3R1, which connects membrane proteins with the underlying actin cytoskeleton, in the proximity interactome of ICAM-1. EBP50 and ICAM-1 form nano-scale domains that overlap in microvilli, from which ICAM-1 regulates EBP50 nano-organization. Indeed, EBP50 expression is required for ICAM-1-mediated control of BC morphogenesis and actomyosin. Our findings indicate that ICAM-1 regulates the dynamics of epithelial apical membrane domains beyond its role as a heterotypic cell-cell adhesion molecule and reveal potential therapeutic strategies for preserving epithelial architecture during inflammatory stress.
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Affiliation(s)
| | | | - Natalia Reglero-Real
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | | | - Ana Cuervo
- Centro Nacional de Biotecnologia (CSIC)MadridSpain
| | | | - Susana Barroso
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | - Gema de Rivas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | | | | | | | - Carlo Manzo
- Facultat de Ciències, Tecnologia i Enginyeries, Universitat de Vic – Universitat Central de Catalunya (UVic-UCC)VicSpain
| | - Jorge Feito
- Servicio de Anatomía Patológica, Hospital Universitario de SalamancaSalamancaSpain
| | - Germán Andrés
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | - Francisca Molina-Jiménez
- Molecular Biology Unit, Hospital Universitario de la PrincesaMadridSpain
- Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa)MadridSpain
| | - Pedro Majano
- Molecular Biology Unit, Hospital Universitario de la PrincesaMadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
- Department of Cellular Biology, Universidad Complutense de MadridMadridSpain
| | - Isabel Correas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | | | - Sussan Nourshargh
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jaime Millán
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
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7
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [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: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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8
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Zheng H, Wang S, Li X, Hu H. A computational modeling of pri-miRNA expression. PLoS One 2024; 19:e0290768. [PMID: 38165860 PMCID: PMC10760784 DOI: 10.1371/journal.pone.0290768] [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: 06/26/2022] [Accepted: 08/15/2023] [Indexed: 01/04/2024] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in gene regulation. Most studies focus on mature miRNAs, which leaves many unknowns about primary miRNAs (pri-miRNAs). To fill the gap, we attempted to model the expression of pri-miRNAs in 1829 primary cell types, cell lines, and tissues in this study. We demonstrated that the expression of pri-miRNAs can be modeled well by the expression of specific sets of mRNAs, which we termed their associated mRNAs. These associated mRNAs differ from their corresponding target mRNAs and are enriched with specific functions. Most associated mRNAs of a miRNA are shared across conditions, while on average, about one-fifth of the associated mRNAs are condition-specific. Our study shed new light on understanding miRNA biogenesis and general gene transcriptional regulation.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
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9
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Kariotis S, Tan PF, Lu H, Rhodes CJ, Wilkins MR, Lawrie A, Wang D. Omada: robust clustering of transcriptomes through multiple testing. Gigascience 2024; 13:giae039. [PMID: 38991852 PMCID: PMC11238428 DOI: 10.1093/gigascience/giae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/09/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Cohort studies increasingly collect biosamples for molecular profiling and are observing molecular heterogeneity. High-throughput RNA sequencing is providing large datasets capable of reflecting disease mechanisms. Clustering approaches have produced a number of tools to help dissect complex heterogeneous datasets, but selecting the appropriate method and parameters to perform exploratory clustering analysis of transcriptomic data requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent. To address this, we have developed Omada, a suite of tools aiming to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning-based functions. FINDINGS The efficiency of each tool was tested with 7 datasets characterized by different expression signal strengths to capture a wide spectrum of RNA expression datasets. Our toolkit's decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Within datasets with less clear biological distinctions, our tools either formed stable subgroups with different expression profiles and robust clinical associations or revealed signs of problematic data such as biased measurements. CONCLUSIONS In conclusion, Omada successfully automates the robust unsupervised clustering of transcriptomic data, making advanced analysis accessible and reliable even for those without extensive machine learning expertise. Implementation of Omada is available at http://bioconductor.org/packages/omada/.
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Affiliation(s)
- Sokratis Kariotis
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Pei Fang Tan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
| | - Haiping Lu
- Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, S1 4DP, Sheffield, United Kingdom
| | - Christopher J Rhodes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Martin R Wilkins
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Allan Lawrie
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Dennis Wang
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
- Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, S1 4DP, Sheffield, United Kingdom
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10
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Muntiu A, Papait A, Vincenzoni F, Vitali A, Lattanzi W, Romele P, Cargnoni A, Silini A, Parolini O, Desiderio C. Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization. Stem Cell Res Ther 2023; 14:339. [PMID: 38012707 PMCID: PMC10683150 DOI: 10.1186/s13287-023-03557-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The secretome of mesenchymal stromal cells isolated from the amniotic membrane (hAMSCs) has been extensively studied for its in vitro immunomodulatory activity as well as for the treatment of several preclinical models of immune-related disorders. The bioactive molecules within the hAMSCs secretome are capable of modulating the immune response and thus contribute to stimulating regenerative processes. At present, only a few studies have attempted to define the composition of the secretome, and several approaches, including multi-omics, are underway in an attempt to precisely define its composition and possibly identify key factors responsible for the therapeutic effect. METHODS In this study, we characterized the protein composition of the hAMSCs secretome by a filter-aided sample preparation (FASP) digestion and liquid chromatography-high resolution mass spectrometry (LC-MS) approach. Data were processed for gene ontology classification and functional protein interaction analysis by bioinformatics tools. RESULTS Proteomic analysis of the hAMSCs secretome resulted in the identification of 1521 total proteins, including 662 unique elements. A number of 157 elements, corresponding to 23.7%, were found as repeatedly characterizing the hAMSCs secretome, and those that resulted as significantly over-represented were involved in immunomodulation, hemostasis, development and remodeling of the extracellular matrix molecular pathways. CONCLUSIONS Overall, our characterization enriches the landscape of hAMSCs with new information that could enable a better understanding of the mechanisms of action underlying the therapeutic efficacy of the hAMSCs secretome while also providing a basis for its therapeutic translation.
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Affiliation(s)
- Alexandra Muntiu
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) ''Giulio Natta'', Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Andrea Papait
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy
| | - Federica Vincenzoni
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alberto Vitali
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) ''Giulio Natta'', Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Wanda Lattanzi
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy
| | - Pietro Romele
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Italy
| | - Anna Cargnoni
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Italy
| | - Antonietta Silini
- Centro di Ricerca E. Menni, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Italy
| | - Ornella Parolini
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy.
- Fondazione Policlinico Universitario ''Agostino Gemelli'' Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS, Rome, Italy.
| | - Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) ''Giulio Natta'', Consiglio Nazionale delle Ricerche, Rome, Italy.
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11
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Long D, Zhang R, Du C, Tong J, Ni Y, Zhou Y, Zuo Y, Liao M. Integrated analysis of the ubiquitination mechanism reveals the specific signatures of tissue and cancer. BMC Genomics 2023; 24:523. [PMID: 37667177 PMCID: PMC10478310 DOI: 10.1186/s12864-023-09583-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/13/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Ubiquitination controls almost all cellular processes. The dysregulation of ubiquitination signals is closely associated with the initiation and progression of multiple diseases. However, there is little comprehensive research on the interaction and potential function of ubiquitination regulators (UBRs) in spermatogenesis and cancer. METHODS We systematically characterized the mRNA and protein expression of UBRs across tissues and further evaluated their roles in testicular development and spermatogenesis. Subsequently, we explored the genetic alterations, expression perturbations, cancer hallmark-related pathways, and clinical relevance of UBRs in pan-cancer. RESULTS This work reveals heterogeneity in the expression patterns of UBRs across tissues, and the expression pattern in testis is the most distinct. UBRs are dynamically expressed during testis development, which are critical for normal spermatogenesis. Furthermore, UBRs have widespread genetic alterations and expression perturbations in pan-cancer. The expression of 79 UBRs was identified to be closely correlated with the activity of 32 cancer hallmark-related pathways, and ten hub genes were screened for further clinical relevance analysis by a network-based method. More than 90% of UBRs can affect the survival of cancer patients, and hub genes have an excellent prognostic classification for specific cancer types. CONCLUSIONS Our study provides a comprehensive analysis of UBRs in spermatogenesis and pan-cancer, which can build a foundation for understanding male infertility and developing cancer drugs in the aspect of ubiquitination.
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Affiliation(s)
- Deyu Long
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, 010070, Hohhot, China
| | - Ruiqi Zhang
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Changjian Du
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Jiapei Tong
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Ni
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Yaqi Zhou
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, 010070, Hohhot, China.
| | - Mingzhi Liao
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, China.
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12
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Shi X, Hu Z, Gan B, He Y, Zhang L, Chen M, Wang Y, Li X. Multivariate Evaluation of DNA Quality Differences in Different Preanalytical Procedures in Mouse Livers. Biopreserv Biobank 2023; 21:378-387. [PMID: 36067273 DOI: 10.1089/bio.2022.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Successful histogenetic research relies on proper handling of tissue samples to maximize DNA quality. As the largest gland in the body, the liver is particularly sensitive to sample mishandling owing to its enzymatic and transcriptional activity. However, the impact of preanalytical procedures on the quality of extracted liver DNA remains poorly understood. In this study, we assessed the impact of extraction methods, duration of ex vivo liver ischemia, liver storage time, and temperature on extracted DNA quality. Comprehensive parameters such as DNA yields, purity, DNA integrity number, the percentage of double-stranded DNA (%dsDNA), and PCR amplification of the GAPDH gene fragment were assessed to identify the quality of extracted DNA. Our results revealed that these preanalytical processes had little effect on DIN values and PCR efficiency of GAPDH gene fragments for each sample, whereas the DNA yields, purity, and %dsDNAs varied widely across different processes. For liver DNA extraction, RNase is necessary to isolate "pure" DNA, and the presence of RNase could significantly increase the %dsDNA. In addition, significant increases in the yields, purity, and %dsDNA of extracted DNA were observed in the TissueLyser-processed livers compared with the mortar and pestle or shear cell disruption methods. Further investigation revealed that livers experiencing longer periods of ex vivo ischemia resulted in significantly compromised DNA yields, and to obtain sufficient DNA, the ex vivo liver ischemia should be limited to within 30 minutes. Moreover, compared with storage of livers at -80°C, storage of livers in the vapor phase of liquid nitrogen yielded a higher quality of the extracted DNA. Our findings exhibited significant implications for liver-derived DNA quality assessment and management.
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Affiliation(s)
- Xue Shi
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yinlin He
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Min Chen
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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13
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Walker LC, Hoya MDL, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet 2023; 110:1046-1067. [PMID: 37352859 PMCID: PMC10357475 DOI: 10.1016/j.ajhg.2023.06.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1, PS3, PP3, BS3, BP4, and BP7. However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. We utilized empirically derived splicing evidence to (1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, (2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and (3) exemplify methodology to calibrate splice prediction tools. We propose repurposing the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely, BP7 may be used to capture RNA results demonstrating no splicing impact for intronic and synonymous variants. We propose that the PS3/BS3 codes are applied only for well-established assays that measure functional impact not directly captured by RNA-splicing assays. We recommend the application of PS1 based on similarity of predicted RNA-splicing effects for a variant under assessment in comparison with a known pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA-assay evidence described aim to help standardize variant pathogenicity classification processes when interpreting splicing-based evidence.
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Affiliation(s)
- Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | | | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daffodil M Canson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | | | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Steven M Harrison
- Ambry Genetics, Aliso Viejo, CA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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14
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Pai S, Hui S, Weber P, Narayan S, Whitley O, Li P, Labrie V, Baumbach J, Wheeler AL, Bader GD. Multi-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition. Cereb Cortex 2023; 33:8581-8593. [PMID: 37106565 PMCID: PMC10321094 DOI: 10.1093/cercor/bhad142] [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: 01/19/2022] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
An open challenge in human genetics is to better understand the systems-level impact of genotype variation on developmental cognition. To characterize the genetic underpinnings of peri-adolescent cognition, we performed genotype-phenotype and systems analysis for binarized accuracy in nine cognitive tasks from the Philadelphia Neurodevelopmental Cohort (~2,200 individuals of European continental ancestry aged 8-21 years). We report a region of genome-wide significance within the 3' end of the Fibulin-1 gene (P = 4.6 × 10-8), associated with accuracy in nonverbal reasoning, a heritable form of complex reasoning ability. Diffusion tensor imaging data from a subset of these participants identified a significant association of white matter fractional anisotropy with FBLN1 genotypes (P < 0.025); poor performers show an increase in the C and A allele for rs77601382 and rs5765534, respectively, which is associated with increased fractional anisotropy. Integration of published human brain-specific 'omic maps, including single-cell transcriptomes of the developing human brain, shows that FBLN1 demonstrates greatest expression in the fetal brain, as a marker of intermediate progenitor cells, demonstrates negligible expression in the adolescent and adult human brain, and demonstrates increased expression in the brain in schizophrenia. Collectively these findings warrant further study of this gene and genetic locus in cognition, neurodevelopment, and disease. Separately, genotype-pathway analysis identified an enrichment of variants associated with working memory accuracy in pathways related to development and to autonomic nervous system dysfunction. Top-ranking pathway genes include those genetically associated with diseases with working memory deficits, such as schizophrenia and Parkinson's disease. This work advances the "molecules-to-behavior" view of cognition and provides a framework for using systems-level organization of data for other biomedical domains.
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Affiliation(s)
- Shraddha Pai
- The Donnelly Centre, University of Toronto, Toronto, Canada
- Adaptive Oncology, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Shirley Hui
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Philipp Weber
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Soumil Narayan
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Owen Whitley
- The Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Peipei Li
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, United States
- Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Viviane Labrie
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, United States
- Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Anne L Wheeler
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
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15
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Wu S, Yang F, Chao S, Wang B, Wang W, Li H, Yu L, He L, Li X, Sun L, Qin S. Altered DNA methylome profiles of blood leukocytes in Chinese patients with mild cognitive impairment and Alzheimer's disease. Front Genet 2023; 14:1175864. [PMID: 37388929 PMCID: PMC10300350 DOI: 10.3389/fgene.2023.1175864] [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: 02/28/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Objective: DNA methylation plays a potential role in the pathogenesis of Alzheimer's disease (AD). However, little is known about the global changes of blood leukocyte DNA methylome profiles from Chinese patients with mild cognitive impairment (MCI) and with AD, or the specific DNA methylation-based signatures associated with MCI and AD. In this study, we sought to dissect the characteristics of blood DNA methylome profiles in MCI- and AD-affected Chinese patients with the aim of identifying novel DNA methylation biomarkers for AD. Methods: In this study, we profiled the DNA methylome of peripheral blood leukocytes from 20 MCI- and 20 AD-affected Chinese patients and 20 cognitively healthy controls (CHCs) with the Infinium Methylation EPIC BeadChip array. Results: We identified significant alterations of the methylome profiles in MCI and AD blood leukocytes. A total of 2,582 and 20,829 CpG sites were significantly and differentially methylated in AD and MCI compared with CHCs (adjusted p < 0.05), respectively. Furthermore, 441 differentially methylated positions (DMPs), aligning to 213 unique genes, were overlapped by the three comparative groups of AD versus CHCs, MCI versus CHCs, and AD versus MCI, of which 6 and 5 DMPs were continuously hypermethylated and hypomethylated in MCI and AD relative to CHCs (adjusted p < 0.05), respectively, such as FLNC cg20186636 and AFAP1 cg06758191. The DMPs with an area under the curve >0.900, such as cg18771300, showed high potency for predicting MCI and AD. In addition, gene ontology and pathway enrichment results showed that these overlapping genes were mainly involved in neurotransmitter transport, GABAergic synaptic transmission, signal release from synapse, neurotransmitter secretion, and the regulation of neurotransmitter levels. Furthermore, tissue expression enrichment analysis revealed a subset of potentially cerebral cortex-enriched genes associated with MCI and AD, including SYT7, SYN3, and KCNT1. Conclusion: This study revealed a number of potential biomarkers for MCI and AD, also highlighted the presence of epigenetically dysregulated gene networks that may engage in the underlying pathological events resulting in the onset of cognitive impairment and AD progression. Collectively, this study provides prospective cues for developing therapeutic strategies to improve cognitive impairment and AD course.
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Affiliation(s)
- Shaochang Wu
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Fan Yang
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Shan Chao
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Bo Wang
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wuqian Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - He Li
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Limei Yu
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Liya Sun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Shanghai Mental Health Center, Editorial Office, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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16
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Kodagoda YK, Liyanage DS, Omeka WKM, Kim G, Kim J, Lee J. Identification, expression profiling, and functional characterization of cystatin C from big-belly seahorse (Hippocampus abdominalis). FISH & SHELLFISH IMMUNOLOGY 2023; 138:108804. [PMID: 37207886 DOI: 10.1016/j.fsi.2023.108804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023]
Abstract
Cystatins are natural inhibitors of lysosomal cysteine proteases, including cathepsins B, L, H, and S. Cystatin C (CSTC) is a member of the type 2 cystatin family and is an essential biomarker in the prognosis of several diseases. Emerging evidence suggests the immune regulatory roles of CSTC in antigen presentation, the release of different inflammatory mediators, and apoptosis in various pathophysiologies. In this study, the 390-bp cystatin C (HaCSTC) cDNA from big-belly seahorse (Hippocampus abdominalis) was cloned and characterized by screening the pre-established cDNA library. Based on similarities in sequence, HaCSTC is a homolog of the teleost type 2 cystatin family with putative catalytic cystatin domains, signal peptides, and disulfide bonds. HaCSTC transcripts were ubiquitously expressed in all tested big-belly seahorse tissues, with the highest expression in ovaries. Immune challenge with lipopolysaccharides, polyinosinic:polycytidylic acid, Edwardsiella tarda, and Streptococcus iniae caused significant upregulation in HaCSTC transcript levels. Using a pMAL-c5X expression vector, the 14.29-kDa protein of recombinant HaCSTC (rHaCSTC) was expressed in Escherichia coli BL21 (DE3), and its protease inhibitory activity against papain cysteine protease was determined with the aid of a protease substrate. Papain was competitively blocked by rHaCSTC in a dose-dependent manner. In response to viral hemorrhagic septicemia virus (VHSV) infection, HaCSTC overexpression strongly decreased the expression of VHSV transcripts, pro-inflammatory cytokines, and pro-apoptotic genes; while increasing the expression of anti-apoptotic genes in fathead minnow (FHM) cells. Furthermore, HaCSTC overexpression protected VHSV-infected FHM cells against VHSV-induced apoptosis and increased cell viability. Our findings imply the profound role of HaCSTC against pathogen infections by modulating fish immune responses.
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Affiliation(s)
- Yasara Kavindi Kodagoda
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Center for Genomic Selection in Korean Aquaculture, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - D S Liyanage
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - W K M Omeka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Center for Genomic Selection in Korean Aquaculture, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Gaeun Kim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Center for Genomic Selection in Korean Aquaculture, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Jeongeun Kim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Center for Genomic Selection in Korean Aquaculture, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, 63333, Republic of Korea; Center for Genomic Selection in Korean Aquaculture, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea.
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17
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Walker LC, de la Hoya M, Wiggins GA, Lindy A, Vincent LM, Parsons M, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.24.23286431. [PMID: 36865205 PMCID: PMC9980257 DOI: 10.1101/2023.02.24.23286431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1 (null variant in a gene where loss-of-function is the mechanism of disease), PS3 (functional assays show damaging effect on splicing), PP3 (computational evidence supports a splicing effect), BS3 (functional assays show no damaging effect on splicing), BP4 (computational evidence suggests no splicing impact), and BP7 (silent change with no predicted impact on splicing). However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation (SVI) Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. Our study utilised empirically derived splicing evidence to: 1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, 2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and 3) exemplify methodology to calibrate bioinformatic splice prediction tools. We propose repurposing of the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely BP7 may be used to capture RNA results demonstrating no impact on splicing for both intronic and synonymous variants, and for missense variants if protein functional impact has been excluded. Furthermore, we propose that the PS3 and BS3 codes are applied only for well-established assays that measure functional impact that is not directly captured by RNA splicing assays. We recommend the application of PS1 based on similarity of predicted RNA splicing effects for a variant under assessment in comparison to a known Pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA assay evidence described aim to help standardise variant pathogenicity classification processes and result in greater consistency when interpreting splicing-based evidence.
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18
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Digre A, Lindskog C. The human protein atlas-Integrated omics for single cell mapping of the human proteome. Protein Sci 2023; 32:e4562. [PMID: 36604173 PMCID: PMC9850435 DOI: 10.1002/pro.4562] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/30/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Studying the spatial distribution of proteins provides the basis for understanding the biology, molecular repertoire, and architecture of every human cell. The Human Protein Atlas (HPA) has grown into one of the world's largest biological databases, and in the most recent version, a major update of the structure of the database was performed. The data has now been organized into 10 different comprehensive sections, each summarizing different aspects of the human proteome and the protein-coding genes. In particular, large datasets with information on the single cell type level have been integrated, refining the tissue and cell type specificity and detailing the expression in cell states with an increased resolution. The multi-modal data constitute an important resource for both basic and translational science, and hold promise for integration with novel emerging technologies at the protein and RNA level.
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Affiliation(s)
- Andreas Digre
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
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19
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Spatial transcriptome analysis of long non-coding RNAs reveals tissue specificity and functional roles in cancer. J Zhejiang Univ Sci B 2023; 24:15-31. [PMID: 36632748 PMCID: PMC9837373 DOI: 10.1631/jzus.b2200206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) play a significant role in maintaining tissue morphology and functions, and their precise regulatory effectiveness is closely related to expression patterns. However, the spatial expression patterns of lncRNAs in humans are poorly characterized. Here, we constructed five comprehensive transcriptomic atlases of human lncRNAs covering thousands of major tissue samples in normal and disease states. The lncRNA transcriptomes exhibited high consistency within the same tissues across resources, and even higher complexity in specialized tissues. Tissue-elevated (TE) lncRNAs were identified in each resource and robust TE lncRNAs were refined by integrative analysis. We detected 1 to 4684 robust TE lncRNAs across tissues; the highest number was in testis tissue, followed by brain tissue. Functional analyses of TE lncRNAs indicated important roles in corresponding tissue-related pathways. Moreover, we found that the expression features of robust TE lncRNAs made them be effective biomarkers to distinguish tissues; TE lncRNAs also tended to be associated with cancer, and exhibited differential expression or were correlated with patient survival. In summary, spatial classification of lncRNAs is the starting point for elucidating the function of lncRNAs in both maintenance of tissue morphology and progress of tissue-constricted diseases.
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20
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Du H, Ma J, Zhou W, Li M, Huai C, Shen L, Wu H, Zhao X, Zhang N, Gao S, Wang Q, He L, Wu X, Qin S, Zhao M. Methylome-wide association study of different responses to risperidone in schizophrenia. Front Pharmacol 2022; 13:1078464. [PMID: 36618913 PMCID: PMC9815458 DOI: 10.3389/fphar.2022.1078464] [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: 10/24/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Accumulating evidence shows that DNA methylation plays a role in antipsychotic response. However, the mechanisms by which DNA methylation changes are associated with antipsychotic responses remain largely unknown. Methods: We performed a methylome-wide association study (MWAS) to evaluate the association between DNA methylation and the response to risperidone in schizophrenia. Genomic DNA methylation patterns were assessed using the Agilent Human DNA Methylation Microarray. Results: We identified numerous differentially methylated positions (DMPs) and regions (DMRs) associated with antipsychotic response. CYP46A1, SPATS2, and ATP6V1E1 had the most significant DMPs, with p values of 2.50 × 10-6, 3.53 × 10-6, and 5.71 × 10-6, respectively. The top-ranked DMR was located on chromosome 7, corresponding to the PTPRN2 gene with a Šidák-corrected p-value of 9.04 × 10-13. Additionally, a significant enrichment of synaptic function and neurotransmitters was found in the differentially methylated genes after gene ontology and pathway analysis. Conclusion: The identified DMP- and DMR-overlapping genes associated with antipsychotic response are related to synaptic function and neurotransmitters. These findings may improve understanding of the mechanisms underlying antipsychotic response and guide the choice of antipsychotic in schizophrenia.
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Affiliation(s)
- Huihui Du
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Jingsong Ma
- School o f Engineering, Westlake University, Hangzhou, Zhejiang, China,Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xianglong Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Na Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Songyin Gao
- Zhumadian Psychiatric Hospital, Zhumadian, China
| | - Qi Wang
- Hebei Mental Health Center, Hebei Sixth People’s Hospital, Baoding, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xuming Wu
- Nantong Fourth People’s Hospital, Nantong, China,*Correspondence: Xuming Wu, ; Shengying Qin, ; Mingzhe Zhao,
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Xuming Wu, ; Shengying Qin, ; Mingzhe Zhao,
| | - Mingzhe Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education, Shanghai Jiao Tong University, Shanghai, China,Affiliated Mental Health Center and Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Xuming Wu, ; Shengying Qin, ; Mingzhe Zhao,
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21
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Noltes ME, Sondorp LH, Kracht L, Antunes IF, Wardenaar R, Kelder W, Kemper A, Szymanski W, Zandee WT, Jansen L, Brouwers AH, Coppes RP, Kruijff S. Patient-derived parathyroid organoids as a tracer and drug-screening application model. Stem Cell Reports 2022; 17:2518-2530. [PMID: 36306782 PMCID: PMC9669499 DOI: 10.1016/j.stemcr.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022] Open
Abstract
Parathyroid diseases are characterized by dysregulation of calcium homeostasis and alterations in parathyroid hormone (PTH) excretion. The development of parathyroid-targeted treatment and imaging tracers could benefit from in vitro models. Therefore, we aim to establish a patient-derived parathyroid organoid model representing human parathyroid tissue. Hyperplastic parathyroid tissue was dispersed, and parathyroid organoids (PTOs) were cultured and characterized. PTO-derived cells exhibited self-renewal over several passages, indicative of the presence of putative stem cells. Immunofluorescence and RNA sequencing confirmed that PTOs phenocopy hyperplastic parathyroid tissue. Exposure of PTOs to increasing calcium concentrations and PTH-lowering drugs resulted in significantly reduced PTH excretion. PTOs showed specific binding of the imaging tracers 11C-methionine and 99mTc-sestamibi. These data show the functionality of PTOs resembling the parathyroid. This PTO model recapitulates the originating tissue on gene and protein expression and functionality, paving the way for future physiology studies and therapeutic target and tracer discovery.
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22
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Santos-Durán GN, Barreiro-Iglesias A. Roles of dual specificity tyrosine-phosphorylation-regulated kinase 2 in nervous system development and disease. Front Neurosci 2022; 16:994256. [PMID: 36161154 PMCID: PMC9492948 DOI: 10.3389/fnins.2022.994256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Dual specificity tyrosine-phosphorylation-regulated kinases (DYRKs) are a group of conserved eukaryotic kinases phosphorylating tyrosine, serine, and threonine residues. The human DYRK family comprises 5 members (DYRK1A, DYRK1B, DYRK2, DYRK3, and DYRK4). The different DYRKs have been implicated in neurological diseases, cancer, and virus infection. Specifically, DYRK2 has been mainly implicated in cancer progression. However, its role in healthy and pathological nervous system function has been overlooked. In this context, we review current available data on DYRK2 in the nervous system, where the available studies indicate that it has key roles in neuronal development and function. DYRK2 regulates neuronal morphogenesis (e.g., axon growth and branching) by phosphorylating cytoskeletal elements (e.g., doublecortin). Comparative data reveals that it is involved in the development of olfactory and visual systems, the spinal cord and possibly the cortex. DYRK2 also participates in processes such as olfaction, vision and, learning. However, DYRK2 could be involved in other brain functions since available expression data shows that it is expressed across the whole brain. High DYRK2 protein levels have been detected in basal ganglia and cerebellum. In adult nervous system, DYRK2 mRNA expression is highest in the cortex, hippocampus, and retina. Regarding nervous system disease, DYRK2 has been implicated in neuroblastoma, glioma, epilepsy, neuroinflammation, Alzheimer's disease, Parkinson's disease, spinal cord injury and virus infection. DYRK2 upregulation usually has a negative impact in cancer-related conditions and a positive impact in non-malignant conditions. Its role in axon growth makes DYRK2 as a promising target for spinal cord or brain injury and regeneration.
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Affiliation(s)
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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23
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Lindskog C, Méar L, Virhammar J, Fällmar D, Kumlien E, Hesselager G, Casar-Borota O, Rostami E. Protein Expression Profile of ACE2 in the Normal and COVID-19-Affected Human Brain. J Proteome Res 2022; 21:2137-2145. [PMID: 35901083 PMCID: PMC9364976 DOI: 10.1021/acs.jproteome.2c00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 12/30/2022]
Abstract
SARS-coronavirus 2 (SARS-CoV-2) that caused the coronavirus disease 2019 (COVID-19) pandemic has posed to be a global challenge. An increasing number of neurological symptoms have been linked to the COVID-19 disease, but the underlying mechanisms of such symptoms and which patients could be at risk are not yet established. The suggested key receptor for host cell entry is angiotensin I converting enzyme 2 (ACE2). Previous studies on limited tissue material have shown no or low protein expression of ACE2 in the normal brain. Here, we used stringently validated antibodies and immunohistochemistry to examine the protein expression of ACE2 in all major regions of the normal brain. The expression pattern was compared with the COVID-19-affected brain of patients with a varying degree of neurological symptoms. In the normal brain, the expression was restricted to the choroid plexus and ependymal cells with no expression in any other brain cell types. Interestingly, in the COVID-19-affected brain, an upregulation of ACE2 was observed in endothelial cells of certain patients, most prominently in the white matter and with the highest expression observed in the patient with the most severe neurological symptoms. The data shows differential expression of ACE2 in the diseased brain and highlights the need to further study the role of endothelial cells in COVID-19 disease in relation to neurological symptoms.
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Affiliation(s)
- Cecilia Lindskog
- Department
of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Loren Méar
- Department
of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Johan Virhammar
- Department
of Neuroscience, Neurology, Uppsala University, 751 85 Uppsala, Sweden
| | - David Fällmar
- Department
of Surgical Sciences, Radiology, Uppsala
University, 751 85 Uppsala, Sweden
| | - Eva Kumlien
- Department
of Neuroscience, Neurology, Uppsala University, 751 85 Uppsala, Sweden
| | - Göran Hesselager
- Department
of Neuroscience, Neurosurgery, Uppsala University, 751 85 Uppsala, Sweden
| | - Olivera Casar-Borota
- Department
of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
- Department
of Clinical Pathology and Cytology, Uppsala
University Hospital, 751
85 Uppsala, Sweden
| | - Elham Rostami
- Department
of Neuroscience, Neurosurgery, Uppsala University, 751 85 Uppsala, Sweden
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24
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Hu Y, Zhang Y, Liu Y, Gao Y, San T, Li X, Song S, Yan B, Zhao Z. Advances in application of single-cell RNA sequencing in cardiovascular research. Front Cardiovasc Med 2022; 9:905151. [PMID: 35958408 PMCID: PMC9360414 DOI: 10.3389/fcvm.2022.905151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides high-resolution information on transcriptomic changes at the single-cell level, which is of great significance for distinguishing cell subtypes, identifying stem cell differentiation processes, and identifying targets for disease treatment. In recent years, emerging single-cell RNA sequencing technologies have been used to make breakthroughs regarding decoding developmental trajectories, phenotypic transitions, and cellular interactions in the cardiovascular system, providing new insights into cardiovascular disease. This paper reviews the technical processes of single-cell RNA sequencing and the latest progress based on single-cell RNA sequencing in the field of cardiovascular system research, compares single-cell RNA sequencing with other single-cell technologies, and summarizes the extended applications and advantages and disadvantages of single-cell RNA sequencing. Finally, the prospects for applying single-cell RNA sequencing in the field of cardiovascular research are discussed.
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Affiliation(s)
- Yue Hu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Ying Zhang
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Yutong Liu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Yan Gao
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Tiantian San
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Xiaoying Li
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- Department of Emergency, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Sensen Song
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Binglong Yan
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Zhuo Zhao
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- *Correspondence: Zhuo Zhao
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25
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Wang S, Zheng H, Choi JS, Lee JK, Li X, Hu H. A systematic evaluation of the computational tools for ligand-receptor-based cell-cell interaction inference. Brief Funct Genomics 2022; 21:339-356. [PMID: 35822343 PMCID: PMC9479691 DOI: 10.1093/bfgp/elac019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-cell interactions (CCIs) are essential for multicellular organisms to coordinate biological processes and functions. One classical type of CCI interaction is between secreted ligands and cell surface receptors, i.e. ligand-receptor (LR) interactions. With the recent development of single-cell technologies, a large amount of single-cell ribonucleic acid (RNA) sequencing (scRNA-Seq) data has become widely available. This data availability motivated the single-cell-resolution study of CCIs, particularly LR-based CCIs. Dozens of computational methods and tools have been developed to predict CCIs by identifying LR-based CCIs. Many of these tools have been theoretically reviewed. However, there is little study on current LR-based CCI prediction tools regarding their performance and running results on public scRNA-Seq datasets. In this work, to fill this gap, we tested and compared nine of the most recent computational tools for LR-based CCI prediction. We used 15 well-studied scRNA-Seq samples that correspond to approximately 100K single cells under different experimental conditions for testing and comparison. Besides briefing the methodology used in these nine tools, we summarized the similarities and differences of these tools in terms of both LR prediction and CCI inference between cell types. We provided insight into using these tools to make meaningful discoveries in understanding cell communications.
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Affiliation(s)
| | | | | | | | - Xiaoman Li
- Corresponding authors: Haiyan Hu, Department of Computer Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078820134; Fax: +1-4078235835; E-mail: ; Xiaoman Li, Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078234811; Fax: +1-4078235835; E-mail:
| | - Haiyan Hu
- Corresponding authors: Haiyan Hu, Department of Computer Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078820134; Fax: +1-4078235835; E-mail: ; Xiaoman Li, Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA. Tel.: +1-4078234811; Fax: +1-4078235835; E-mail:
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26
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Plasmolipin regulates basolateral-to-apical transcytosis of ICAM-1 and leukocyte adhesion in polarized hepatic epithelial cells. Cell Mol Life Sci 2022; 79:61. [PMID: 34999972 PMCID: PMC8743267 DOI: 10.1007/s00018-021-04095-z] [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: 04/27/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/30/2022]
Abstract
Apical localization of Intercellular Adhesion Receptor (ICAM)-1 regulates the adhesion and guidance of leukocytes across polarized epithelial barriers. Here, we investigate the molecular mechanisms that determine ICAM-1 localization into apical membrane domains of polarized hepatic epithelial cells, and their effect on lymphocyte-hepatic epithelial cell interaction. We had previously shown that segregation of ICAM-1 into apical membrane domains, which form bile canaliculi and bile ducts in hepatic epithelial cells, requires basolateral-to-apical transcytosis. Searching for protein machinery potentially involved in ICAM-1 polarization we found that the SNARE-associated protein plasmolipin (PLLP) is expressed in the subapical compartment of hepatic epithelial cells in vitro and in vivo. BioID analysis of ICAM-1 revealed proximal interaction between this adhesion receptor and PLLP. ICAM-1 colocalized and interacted with PLLP during the transcytosis of the receptor. PLLP gene editing and silencing increased the basolateral localization and reduced the apical confinement of ICAM-1 without affecting apicobasal polarity of hepatic epithelial cells, indicating that ICAM-1 transcytosis is specifically impaired in the absence of PLLP. Importantly, PLLP depletion was sufficient to increase T-cell adhesion to hepatic epithelial cells. Such an increase depended on the epithelial cell polarity and ICAM-1 expression, showing that the epithelial transcytotic machinery regulates the adhesion of lymphocytes to polarized epithelial cells. Our findings strongly suggest that the polarized intracellular transport of adhesion receptors constitutes a new regulatory layer of the epithelial inflammatory response.
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27
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Yang H, Arif M, Yuan M, Li X, Shong K, Türkez H, Nielsen J, Uhlén M, Borén J, Zhang C, Mardinoglu A. A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease. iScience 2021; 24:103222. [PMID: 34712920 PMCID: PMC8529555 DOI: 10.1016/j.isci.2021.103222] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/16/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver disease worldwide. We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD. Based on network analysis, we identified a highly conserved disease-associated gene module across three different NAFLD cohorts and highlighted the predominant role of key transcriptional regulators associated with lipid and cholesterol metabolism. In addition, we revealed the detailed metabolic differences between heterogeneous NAFLD patients through integrative systems analysis of transcriptomic data and liver-specific genome-scale metabolic model. Furthermore, we identified transcription factors (TFs), including SREBF2, HNF4A, SREBF1, YY1, and KLF13, showing regulation of hepatic expression of genes in the NAFLD-associated modules and validated the TFs using data generated from a mouse NAFLD model. In conclusion, our integrative analysis facilitates the understanding of the regulatory mechanism of these perturbed TFs and their associated biological processes. Disease-associated gene modules are conserved across multiple NAFLD cohorts The central genes in disease-associated modules are key enzymes in cholesterol synthesis YY1 and KLF13 are potential key transcriptional regulators of NAFLD development
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Affiliation(s)
- Hong Yang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Meng Yuan
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Xiangyu Li
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Koeun Shong
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Hasan Türkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden.,BioInnovation Institute, 2200 Copenhagen, Denmark
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Borén
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
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28
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Xue G, Wang Z, Zheng N, Fang J, Mao C, Li X, Jin G, Ming X, Lu Y. Elimination of acquired resistance to PD-1 blockade via the concurrent depletion of tumour cells and immunosuppressive cells. Nat Biomed Eng 2021; 5:1306-1319. [PMID: 34725506 PMCID: PMC8595849 DOI: 10.1038/s41551-021-00799-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
Antigen release resulting from the death of tumour cells induced by chemotherapies and targeted therapies can augment the antitumour responses induced by immune checkpoint blockade (ICB). However, tumours responding to ICB therapies often become resistant to them. Here we show that the specific targeting of tumour cells promotes the growth of tumour-cell variants that are resistant to ICB, and that the acquired resistance can be overcome via the concurrent depletion of tumour cells and of major types of immunosuppressive cell via a monoclonal antibody binding the enzyme CD73, which we identified as highly expressed on tumour cells and on regulatory T cells, myeloid-derived suppressor cells and tumour-associated macrophages, but not on cytolytic T lymphocytes, natural killer cells and dendritic cells. In mice with murine tumours, the systemic administration of anti-PD1 antibodies and anti-CD73 antibodies conjugated to a near-infrared dye prevented near-infrared-irradiated tumours from acquiring resistance to ICB and resulted in the eradication of advanced tumours. The elimination of immunosuppressive cells may overcome acquired resistance to ICB across a range of tumour types and combination therapies.
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Affiliation(s)
- Gang Xue
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Microbiology & Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27101
| | - Ziyu Wang
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Microbiology & Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27101
| | - Ningbo Zheng
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Microbiology & Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27101
| | - Jing Fang
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Microbiology & Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27101
| | - Chengqiong Mao
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27157
| | - Xiaoyin Li
- Department of Mathematics and Statistics, St. Cloud State University, St Cloud, MN, USA, 56301
| | - Guangxu Jin
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27157
| | - Xin Ming
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27157
| | - Yong Lu
- Comprehensive Cancer Center, Wake Forest Baptist Health, Winston-Salem, NC, USA, 27157; Department of Microbiology & Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27101,Corresponding authors, , Correspondence and requests for materials should be addressed to Y.L
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29
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Shen L, Lv X, Huang H, Li M, Huai C, Wu X, Wu H, Ma J, Chen L, Wang T, Tan J, Sun Y, Li L, Shi Y, Yang C, Cai L, Lu Y, Zhang Y, Weng S, Tai S, Zhang N, He L, Wan C, Qin S. Genome-wide analysis of DNA methylation in 106 schizophrenia family trios in Han Chinese. EBioMedicine 2021; 72:103609. [PMID: 34628353 PMCID: PMC8511801 DOI: 10.1016/j.ebiom.2021.103609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/05/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022] Open
Abstract
Background Schizophrenia (SCZ) is a severe psychiatric disorder that affects approximately 0.75% of the global population. Both genetic and environmental factors contribute to development of SCZ. SCZ tends to run in family while both genetic and environmental factor contribute to its etiology. Much evidence suggested that alterations in DNA methylations occurred in SCZ patients. Methods To investigate potential inheritable pattern of DNA methylation in SCZ family, we performed a genome-wide analysis of DNA methylation of peripheral blood samples from 106 Chinese SCZ family trios. Genome-wide DNA methylations were quantified by Agilent 1 × 244 k Human Methylation Microarray. Findings In this study, we proposed a loci inheritance frequency model that allows characterization of differential methylated regions as SCZ biomarkers. Based on this model, 112 hypermethylated and 125 hypomethylated regions were identified. Additionally, 121 hypermethylated and 139 hypomethylated genes were annotated. The results of functional enrichment analysis indicated that multiple differentially methylated genes (DMGs) involved in Notch/HH/Wnt signaling, MAPK signaling, GPCR signaling, immune response signaling. Notably, a number of hypomethylated genes were significantly enriched in cerebral cortex and functionally enriched in nervous system development. Interpretation Our findings not only validated previously discovered risk genes of SCZ but also identified novel candidate DMGs in SCZ. These results may further the understanding of altered DNA methylations in SCZ.
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Affiliation(s)
- Lu Shen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaoying Lv
- DCH Technologies Inc, Cambridge, MA 02142, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences, Shanghai 200031, PR China; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mo Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Cong Huai
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Xi Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Hao Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Jingsong Ma
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Luan Chen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Ting Wang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Jie Tan
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Yidan Sun
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Lixing Li
- Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Chao Yang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Lei Cai
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Yana Lu
- Wuxi Mental Health Center, Nanjing Medical University, Wuxi 214151, China
| | - Yan Zhang
- The Second People's Hospital of Lishui, Lishui 323020, China
| | - Saizheng Weng
- Fuzhou Neuro-psychiatric hospital, Fujian Medical University, Fuzhou 350026, China
| | - Shaobin Tai
- The Second People's Hospital of Huangshan, Huangshan 245021, China
| | - Na Zhang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Lin He
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China; Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Chunling Wan
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China.
| | - Shengying Qin
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China.
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30
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Manatakis DV, VanDevender A, Manolakos ES. An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures. Bioinformatics 2021; 36:5194-5204. [PMID: 32683449 PMCID: PMC7850114 DOI: 10.1093/bioinformatics/btaa654] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/26/2020] [Accepted: 07/14/2020] [Indexed: 12/02/2022] Open
Abstract
Motivation Recapitulating aspects of human organ functions using in vitro (e.g.
plates, transwells, etc.), in vivo (e.g. mouse, rat, etc.), or
ex vivo (e.g. organ chips, 3D systems, etc.) organ models is of
paramount importance for drug discovery and precision medicine. It will allow us to
identify potential side effects and test the effectiveness of new therapeutic approaches
early in their design phase, and will inform the development of better disease models.
Developing mathematical methods to reliably compare the ‘distance/similarity’ of organ
models from/to the real human organ they represent is an understudied problem with
important applications in biomedicine and tissue engineering. Results We introduce the Transcriptomic Signature Distance (TSD), an
information-theoretic distance for assessing the transcriptomic similarity of two tissue
samples, or two groups of tissue samples. In developing TSD, we are
leveraging next-generation sequencing data as well as information retrieved from
well-curated databases providing signature gene sets characteristic for human organs. We
present the justification and mathematical development of the new distance and
demonstrate its effectiveness and advantages in different scenarios of practical
importance using several publicly available RNA-seq datasets. Availability and Implementation The computation of both TSD versions (simple and weighted) has been
implemented in R and can be downloaded from
https://github.com/Cod3B3nd3R/Transcriptomic-Signature-Distance. Contact dimitris.manatakis@emulatebio.com Supplementary information Supplementary data are
available at Bioinformatics online.
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Affiliation(s)
| | | | - Elias S Manolakos
- Department of Informatics and Telecommunications, University of Athens, Athens 15784, Greece.,Bouve College of Health Sciences, Northeastern University, Boston, MA 02115, USA
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31
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Afshar Y, Dong J, Zhao P, Li L, Wang S, Zhang RY, Zhang C, Yin O, Han CS, Einerson BD, Gonzalez TL, Zhang H, Zhou A, Yang Z, Chou SJ, Sun N, Cheng J, Zhu H, Wang J, Zhang TX, Lee YT, Wang JJ, Teng PC, Yang P, Qi D, Zhao M, Sim MS, Zhe R, Goldstein JD, Williams J, Wang X, Zhang Q, Platt LD, Zou C, Pisarska MD, Tseng HR, Zhu Y. Circulating trophoblast cell clusters for early detection of placenta accreta spectrum disorders. Nat Commun 2021; 12:4408. [PMID: 34344888 PMCID: PMC8333096 DOI: 10.1038/s41467-021-24627-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/21/2021] [Indexed: 11/21/2022] Open
Abstract
Placenta accreta spectrum (PAS) is a high-risk obstetrical condition associated with significant morbidity and mortality. Current clinical screening modalities for PAS are not always conclusive. Here, we report a nanostructure-embedded microchip that efficiently enriches both single and clustered circulating trophoblasts (cTBs) from maternal blood for detecting PAS. We discover a uniquely high prevalence of cTB-clusters in PAS and subsequently optimize the device to preserve the intactness of these clusters. Our feasibility study on the enumeration of cTBs and cTB-clusters from 168 pregnant women demonstrates excellent diagnostic performance for distinguishing PAS from non-PAS. A logistic regression model is constructed using a training cohort and then cross-validated and tested using an independent cohort. The combined cTB assay achieves an Area Under ROC Curve of 0.942 (throughout gestation) and 0.924 (early gestation) for distinguishing PAS from non-PAS. Our assay holds the potential to improve current diagnostic modalities for the early detection of PAS.
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Affiliation(s)
- Yalda Afshar
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jiantong Dong
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Pan Zhao
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Lei Li
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Shan Wang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Ryan Y Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ceng Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ophelia Yin
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christina S Han
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Fetal Medicine and Women's Ultrasound, Los Angeles, CA, USA
| | - Brett D Einerson
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, University of Utah Health, Salt Lake City, UT, USA
| | - Tania L Gonzalez
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Huirong Zhang
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Anqi Zhou
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhuo Yang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shih-Jie Chou
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Na Sun
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ju Cheng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Henan Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jing Wang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tiffany X Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yi-Te Lee
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jasmine J Wang
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Pai-Chi Teng
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Peng Yang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dongping Qi
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Myung-Shin Sim
- Departments of Computational Medicine & Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ruilian Zhe
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Jeffrey D Goldstein
- Department of Pathology and Laboratory Medicine, Ronald Reagan Medical Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John Williams
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xietong Wang
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Qingying Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lawrence D Platt
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Fetal Medicine and Women's Ultrasound, Los Angeles, CA, USA
| | - Chang Zou
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China.
| | - Margareta D Pisarska
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.
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32
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Johari M, Sarparanta J, Vihola A, Jonson PH, Savarese M, Jokela M, Torella A, Piluso G, Said E, Vella N, Cauchi M, Magot A, Magri F, Mauri E, Kornblum C, Reimann J, Stojkovic T, Romero NB, Luque H, Huovinen S, Lahermo P, Donner K, Comi GP, Nigro V, Hackman P, Udd B. Missense mutations in small muscle protein X-linked (SMPX) cause distal myopathy with protein inclusions. Acta Neuropathol 2021; 142:375-393. [PMID: 33974137 PMCID: PMC8270885 DOI: 10.1007/s00401-021-02319-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 01/05/2023]
Abstract
Using
deep phenotyping and high-throughput sequencing, we have identified a novel type of distal myopathy caused by mutations in the Small muscle protein X-linked (SMPX) gene. Four different missense mutations were identified in ten patients from nine families in five different countries, suggesting that this disease could be prevalent in other populations as well. Haplotype analysis of patients with similar ancestry revealed two different founder mutations in Southern Europe and France, indicating that the prevalence in these populations may be higher. In our study all patients presented with highly similar clinical features: adult-onset, usually distal more than proximal limb muscle weakness, slowly progressing over decades with preserved walking. Lower limb muscle imaging showed a characteristic pattern of muscle involvement and fatty degeneration. Histopathological and electron microscopic analysis of patient muscle biopsies revealed myopathic findings with rimmed vacuoles and the presence of sarcoplasmic inclusions, some with amyloid-like characteristics. In silico predictions and subsequent cell culture studies showed that the missense mutations increase aggregation propensity of the SMPX protein. In cell culture studies, overexpressed SMPX localized to stress granules and slowed down their clearance.
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Affiliation(s)
- Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland.
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland.
| | - Jaakko Sarparanta
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Anna Vihola
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Center, Fimlab Laboratories, Tampere University and University Hospital, Tampere, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Manu Jokela
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, Tampere, Finland
- Division of Clinical Neurosciences, Department of Neurology, Turku University Hospital, Turku, Finland
| | - Annalaura Torella
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Giulio Piluso
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Edith Said
- Section of Medical Genetics, Mater Dei Hospital, Msida, Malta
- Department of Anatomy and Cell Biology, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Norbert Vella
- Neuroscience Department, Mater Dei Hospital, Msida, Malta
| | - Marija Cauchi
- Neuroscience Department, Mater Dei Hospital, Msida, Malta
| | - Armelle Magot
- Neuromuscular Disease Center AOC, University Hospital Nantes, Nantes, France
| | - Francesca Magri
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | - Eleonora Mauri
- IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Neurology Unit, Milan, Italy
| | | | - Jens Reimann
- Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Tanya Stojkovic
- AP-HP, Institute of Myology, Centre de Référence des Maladies Neuromusculaires, Hôpital Pitié-Salpêtrière, Paris, France
| | - Norma B Romero
- Neuromuscular Morphology Unit, Institute of Myology, Myology Research Centre INSERM, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Helena Luque
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Sanna Huovinen
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Päivi Lahermo
- Institute for Molecular Medicine Finland FIMM, Technology Centre, University of Helsinki, Helsinki, Finland
| | - Kati Donner
- Institute for Molecular Medicine Finland FIMM, Technology Centre, University of Helsinki, Helsinki, Finland
| | - Giacomo Pietro Comi
- IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Neuromuscular and Rare Disease Unit, Milan, Italy
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Vincenzo Nigro
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, Tampere, Finland
- Department of Neurology, Vaasa Central Hospital, Vaasa, Finland
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Miyashita Y, Tsukamoto O, Matsuoka K, Kamikubo K, Kuramoto Y, Ying Fu H, Tsubota T, Hasuike H, Takayama T, Ito H, Hitsumoto T, Okamoto C, Kioka H, Oya R, Shinomiya H, Hakui H, Shintani Y, Kato H, Kitakaze M, Sakata Y, Asano Y, Takashima S. The CR9 element is a novel mechanical load-responsive enhancer that regulates natriuretic peptide genes expression. FASEB J 2021; 35:e21495. [PMID: 33689182 DOI: 10.1096/fj.202002111rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/11/2022]
Abstract
Enhancers regulate gene expressions in a tissue- and pathology-specific manner by altering its activities. Plasma levels of atrial and brain natriuretic peptides, encoded by the Nppa and Nppb, respectively, and synthesized predominantly in cardiomyocytes, vary depending on the severity of heart failure. We previously identified the noncoding conserved region 9 (CR9) element as a putative Nppb enhancer at 22-kb upstream from the Nppb gene. However, its regulatory mechanism remains unknown. Here, we therefore investigated the mechanism of CR9 activation in cardiomyocytes using different kinds of drugs that induce either cardiac hypertrophy or cardiac failure accompanied by natriuretic peptides upregulation. Chronic treatment of mice with either catecholamines or doxorubicin increased CR9 activity during the progression of cardiac hypertrophy to failure, which is accompanied by proportional increases in Nppb expression. Conversely, for cultured cardiomyocytes, doxorubicin decreased CR9 activity and Nppb expression, while catecholamines increased both. However, exposing cultured cardiomyocytes to mechanical loads, such as mechanical stretch or hydrostatic pressure, upregulate CR9 activity and Nppb expression even in the presence of doxorubicin. Furthermore, the enhancement of CR9 activity and Nppa and Nppb expressions by either catecholamines or mechanical loads can be blunted by suppressing mechanosensing and mechanotransduction pathways, such as muscle LIM protein (MLP) or myosin tension. Finally, the CR9 element showed a more robust and cell-specific response to mechanical loads than the -520-bp BNP promoter. We concluded that the CR9 element is a novel enhancer that responds to mechanical loads by upregulating natriuretic peptides expression in cardiomyocytes.
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Affiliation(s)
- Yohei Miyashita
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan.,Department of Legal Medicine, Graduate School of Medicine, Osaka University, Suita, Japan.,Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Osamu Tsukamoto
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Ken Matsuoka
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Kenta Kamikubo
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Yuki Kuramoto
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hai Ying Fu
- Department of Cardiorenal and Cerebrovascular Medicine, Faculty of Medicine, Kagawa University, Takamatsu, Japan
| | - Tomoya Tsubota
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Hirona Hasuike
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Toshio Takayama
- School of Engineering, Department of Mechanical Engineering, Tokyo Institute of Technology, Tokyo, Japan
| | - Hiroaki Ito
- Department of Physics, Graduate School of Science, Chiba University, Chiba, Japan
| | - Tatsuro Hitsumoto
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Chisato Okamoto
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Hidetaka Kioka
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Ryohei Oya
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Haruki Shinomiya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hideyuki Hakui
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yasunori Shintani
- Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Hisakazu Kato
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | | | - Yasushi Sakata
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Seiji Takashima
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
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34
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Shamie I, Duttke SH, Karottki KJLC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform 2021; 3:lqab061. [PMID: 34268494 PMCID: PMC8276764 DOI: 10.1093/nargab/lqab061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene Mgat3, facilitate activating silent genes by CRISPRa. Together, we envision our revised annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.
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Affiliation(s)
- Isaac Shamie
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Sascha H Duttke
- Department of Medicine, University of California, San Diego 92093, USA
| | - Karen J la Cour Karottki
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Anders H Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Hooman Hefzi
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Kai Xiong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Shangzhong Li
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Samuel J Roth
- Department of Medicine, University of California, San Diego 92093, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Gyun Min Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | | | | | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
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Chen YJC, Dent SYR. Conservation and diversity of the eukaryotic SAGA coactivator complex across kingdoms. Epigenetics Chromatin 2021; 14:26. [PMID: 34112237 PMCID: PMC8194025 DOI: 10.1186/s13072-021-00402-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/03/2021] [Indexed: 12/27/2022] Open
Abstract
The SAGA complex is an evolutionarily conserved transcriptional coactivator that regulates gene expression through its histone acetyltransferase and deubiquitylase activities, recognition of specific histone modifications, and interactions with transcription factors. Multiple lines of evidence indicate the existence of distinct variants of SAGA among organisms as well as within a species, permitting diverse functions to dynamically regulate cellular pathways. Our co-expression analysis of genes encoding human SAGA components showed enrichment in reproductive organs, brain tissues and the skeletal muscle, which corresponds to their established roles in developmental programs, emerging roles in neurodegenerative diseases, and understudied functions in specific cell types. SAGA subunits modulate growth, development and response to various stresses from yeast to plants and metazoans. In metazoans, SAGA further participates in the regulation of differentiation and maturation of both innate and adaptive immune cells, and is associated with initiation and progression of diseases including a broad range of cancers. The evolutionary conservation of SAGA highlights its indispensable role in eukaryotic life, thus deciphering the mechanisms of action of SAGA is key to understanding fundamental biological processes throughout evolution. To illuminate the diversity and conservation of this essential complex, here we discuss variations in composition, essentiality and co-expression of component genes, and its prominent functions across Fungi, Plantae and Animalia kingdoms.
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Affiliation(s)
- Ying-Jiun C Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA.
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Noordam L, Ge Z, Özturk H, Doukas M, Mancham S, Boor PPC, Campos Carrascosa L, Zhou G, van den Bosch TPP, Pan Q, IJzermans JNM, Bruno MJ, Sprengers D, Kwekkeboom J. Expression of Cancer Testis Antigens in Tumor-Adjacent Normal Liver Is Associated with Post-Resection Recurrence of Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13102499. [PMID: 34065388 PMCID: PMC8160719 DOI: 10.3390/cancers13102499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary High recurrence rates after resection of liver cancer (hepatocellular carcinoma) with curative intent impair clinical outcomes of patients diagnosed with liver cancer. Cancer/testis antigens (CTAs) are expressed in cancer and can serve as therapeutic targets. We identified 12 CTAs expressed in 80% of liver cancer patients, and each one individually in at least 10%. Furthermore, we found that patients with expression of CTAs in macroscopically tumor-free liver tissue, experience more tumor recurrence and poor survival after surgical tumor removal. The increased risk of tumor recurrence in patients with CTA expression in tumor-free liver suggests that these patients already have micro-metastasis at the time of operation. These CTA-expressing (pre-)malignant cells may thus be a source of liver cancer recurrence, reflecting the relevance of targeting these to prevent liver cancer recurrence. Abstract High recurrence rates after resection of hepatocellular carcinoma (HCC) with curative intent impair clinical outcomes of HCC. Cancer/testis antigens (CTAs) are suitable targets for cancer immunotherapy if selectively expressed in tumor cells. The aims were to identify CTAs that are frequently and selectively expressed in HCC-tumors, and to investigate whether CTAs could serve as biomarkers for occult metastasis. Tumor and paired tumor-free liver (TFL) tissues of HCC-patients and healthy tissues were assessed for mRNA expression of 49 CTAs by RT-qPCR and protein expression of five CTAs by immunohistochemistry. Twelve CTA-mRNAs were expressed in ≥10% of HCC-tumors and not in healthy tissues except testis. In tumors, mRNA and protein of ≥ 1 CTA was expressed in 78% and 71% of HCC-patients, respectively. In TFL, CTA mRNA and protein was found in 45% and 30% of HCC-patients, respectively. Interestingly, CTA-expression in TFL was an independent negative prognostic factor for post-resection HCC-recurrence and survival. We established a panel of 12 testis-restricted CTAs expressed in tumors of most HCC-patients. The increased risk of HCC-recurrence in patients with CTA expression in TFL, suggests that CTA-expressing (pre-)malignant cells may be a source of HCC-recurrence, reflecting the relevance of targeting these to prevent HCC-recurrence.
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Affiliation(s)
- Lisanne Noordam
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Zhouhong Ge
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Hadiye Özturk
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Michail Doukas
- Department of Pathology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (M.D.); (T.P.P.v.d.B.)
| | - Shanta Mancham
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Patrick P. C. Boor
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Lucia Campos Carrascosa
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Guoying Zhou
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Thierry P. P. van den Bosch
- Department of Pathology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (M.D.); (T.P.P.v.d.B.)
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Jan N. M. IJzermans
- Department of Surgery, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands;
| | - Marco J. Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Dave Sprengers
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
| | - Jaap Kwekkeboom
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, 3000 CA Rotterdam, The Netherlands; (L.N.); (Z.G.); (H.Ö.); (S.M.); (P.P.C.B.); (L.C.C.); (G.Z.); (Q.P.); (M.J.B.); (D.S.)
- Correspondence: ; Tel.: +31-(0)10-703-5942
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Dutt M, Ng YK, Molendijk J, Karimkhanloo H, Liao L, Blazev R, Montgomery MK, Watt MJ, Parker BL. Western Diet Induced Remodelling of the Tongue Proteome. Proteomes 2021; 9:proteomes9020022. [PMID: 34066295 PMCID: PMC8163156 DOI: 10.3390/proteomes9020022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/03/2021] [Accepted: 05/08/2021] [Indexed: 12/14/2022] Open
Abstract
The tongue is a heavily innervated and vascularized striated muscle that plays an important role in vocalization, swallowing and digestion. The surface of the tongue is lined with papillae which contain gustatory cells expressing various taste receptors. There is growing evidence to suggest that our perceptions of taste and food preference are remodelled following chronic consumption of Western diets rich in carbohydrate and fats. Our sensitivity to taste and also to metabolising Western diets may be a key factor in the rising prevalence of obesity; however, a systems-wide analysis of the tongue is lacking. Here, we defined the proteomic landscape of the mouse tongue and quantified changes following chronic consumption of a chow or Western diet enriched in lipid, fructose and cholesterol for 7 months. We observed a dramatic remodelling of the tongue proteome including proteins that regulate fatty acid and mitochondrial metabolism. Furthermore, the expressions of several receptors, metabolic enzymes and hormones were differentially regulated, and are likely to provide novel therapeutic targets to alter taste perception and food preference to combat obesity.
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Narita T, Ito S, Higashijima Y, Chu WK, Neumann K, Walter J, Satpathy S, Liebner T, Hamilton WB, Maskey E, Prus G, Shibata M, Iesmantavicius V, Brickman JM, Anastassiadis K, Koseki H, Choudhary C. Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release. Mol Cell 2021; 81:2166-2182.e6. [PMID: 33765415 DOI: 10.1016/j.molcel.2021.03.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 01/11/2021] [Accepted: 03/04/2021] [Indexed: 12/30/2022]
Abstract
The metazoan-specific acetyltransferase p300/CBP is involved in activating signal-induced, enhancer-mediated transcription of cell-type-specific genes. However, the global kinetics and mechanisms of p300/CBP activity-dependent transcription activation remain poorly understood. We performed genome-wide, time-resolved analyses to show that enhancers and super-enhancers are dynamically activated through p300/CBP-catalyzed acetylation, deactivated by the opposing deacetylase activity, and kinetic acetylation directly contributes to maintaining cell identity at very rapid (minutes) timescales. The acetyltransferase activity is dispensable for the recruitment of p300/CBP and transcription factors but essential for promoting the recruitment of TFIID and RNAPII at virtually all enhancers and enhancer-regulated genes. This identifies pre-initiation complex assembly as a dynamically controlled step in the transcription cycle and reveals p300/CBP-catalyzed acetylation as the signal that specifically promotes transcription initiation at enhancer-regulated genes. We propose that p300/CBP activity uses a "recruit-and-release" mechanism to simultaneously promote RNAPII recruitment and pause release and thereby enables kinetic activation of enhancer-mediated transcription.
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Affiliation(s)
- Takeo Narita
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshiki Higashijima
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Wai Kit Chu
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Katrin Neumann
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jonas Walter
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Shankha Satpathy
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Tim Liebner
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - William B Hamilton
- The Novo Nordisk Foundation Center for Stem Cell Biology-DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Elina Maskey
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Gabriela Prus
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Marika Shibata
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Vytautas Iesmantavicius
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Biology-DanStem, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Immune Regulation, Advanced Research Departments, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark.
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Brown J, Barry C, Schmitz MT, Argus C, Bolin JM, Schwartz MP, Van Aartsen A, Steill J, Swanson S, Stewart R, Thomson JA, Kendziorski C. Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PLoS Comput Biol 2021; 17:e1008778. [PMID: 33647016 PMCID: PMC7951976 DOI: 10.1371/journal.pcbi.1008778] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/11/2021] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Human pluripotent stem cells hold significant promise for regenerative medicine. However, long differentiation protocols and immature characteristics of stem cell-derived cell types remain challenges to the development of many therapeutic applications. In contrast to the slow differentiation of human stem cells in vitro that mirrors a nine-month gestation period, mouse stem cells develop according to a much faster three-week gestation timeline. Here, we tested if co-differentiation with mouse pluripotent stem cells could accelerate the differentiation speed of human embryonic stem cells. Following a six-week RNA-sequencing time course of neural differentiation, we identified 929 human genes that were upregulated earlier and 535 genes that exhibited earlier peaked expression profiles in chimeric cell cultures than in human cell cultures alone. Genes with accelerated upregulation were significantly enriched in Gene Ontology terms associated with neurogenesis, neuron differentiation and maturation, and synapse signaling. Moreover, chimeric mixed samples correlated with in utero human embryonic samples earlier than human cells alone, and acceleration was dose-dependent on human-mouse co-culture ratios. The altered gene expression patterns and developmental rates described in this report have implications for accelerating human stem cell differentiation and the use of interspecies chimeric embryos in developing human organs for transplantation.
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Affiliation(s)
- Jared Brown
- Department of Statistics, University of Wisconsin-Madison, Wisconsin, United States of America
- * E-mail: (JB); (CK)
| | - Christopher Barry
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Matthew T. Schmitz
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Cara Argus
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Jennifer M. Bolin
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Michael P. Schwartz
- NSF Center for Sustainable Nanotechnology, Department of Chemistry, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Amy Van Aartsen
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - John Steill
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Scott Swanson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - James A. Thomson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Wisconsin, United States of America
- * E-mail: (JB); (CK)
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Longitudinal saliva omics responses to immune perturbation: a case study. Sci Rep 2021; 11:710. [PMID: 33436912 PMCID: PMC7804305 DOI: 10.1038/s41598-020-80605-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/23/2020] [Indexed: 01/03/2023] Open
Abstract
Saliva omics has immense potential for non-invasive diagnostics, including monitoring very young or elderly populations, or individuals in remote locations. In this study, multiple saliva omics from an individual were monitored over three periods (100 timepoints) involving: (1) hourly sampling over 24 h without intervention, (2) hourly sampling over 24 h including immune system activation using the standard 23-valent pneumococcal polysaccharide vaccine, (3) daily sampling for 33 days profiling the post-vaccination response. At each timepoint total saliva transcriptome and proteome, and small RNA from salivary extracellular vesicles were profiled, including mRNA, miRNA, piRNA and bacterial RNA. The two 24-h periods were used in a paired analysis to remove daily variation and reveal vaccination responses. Over 18,000 omics longitudinal series had statistically significant temporal trends compared to a healthy baseline. Various immune response and regulation pathways were activated following vaccination, including interferon and cytokine signaling, and MHC antigen presentation. Immune response timeframes were concordant with innate and adaptive immunity development, and coincided with vaccination and reported fever. Overall, mRNA results appeared more specific and sensitive (timewise) to vaccination compared to other omics. The results suggest saliva omics can be consistently assessed for non-invasive personalized monitoring and immune response diagnostics.
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Abstract
Advances in next generation sequencing (NGS) technologies resulted in a broad array of large-scale gene expression studies and an unprecedented volume of whole messenger RNA (mRNA) sequencing data, or the transcriptome (also known as RNA sequencing, or RNA-seq). These include the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA), among others. Here we cover some of the commonly used datasets, provide an overview on how to begin the analysis pipeline, and how to explore and interpret the data provided by these publicly available resources.
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Affiliation(s)
- Yazeed Zoabi
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Mohammed G, Mousa NA, Talaat IM, Ibrahim H, Saber-Ayad M. Breast Cancer Risk with Progestin Subdermal Implants: A Challenge in Patients Counseling. Front Endocrinol (Lausanne) 2021; 12:781066. [PMID: 34975755 PMCID: PMC8719328 DOI: 10.3389/fendo.2021.781066] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/23/2021] [Indexed: 11/27/2022] Open
Abstract
There is a steady global rise in the use of progestin subdermal implants, where use has increased by more than 20 times in the past two decades. BC risk has been reported with the older progestin only methods such as oral pills, injectables, and intrauterine devices, however, little is known about the risk with subdermal implants. In this review, we aim to update clinicians and researchers on the current evidence to support patient counseling and to inform future research directions. The available evidence of the association between the use of progestin subdermal implants and BC risk is discussed. We provide an overview of the potential role of endogenous progesterone in BC development. The chemical structure and molecular targets of synthetic progestins of relevance are summarized together with the preclinical and clinical evidence on their association with BC risk. We review all studies that investigated the action of the specific progestins included in subdermal implants. As well, we discuss the potential effect of the use of subdermal implants in women at increased BC risk, including carriers of BC susceptibility genetic mutations.
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Affiliation(s)
- Ghada Mohammed
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- *Correspondence: Ghada Mohammed, ; Noha A. Mousa,
| | - Noha A. Mousa
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- *Correspondence: Ghada Mohammed, ; Noha A. Mousa,
| | - Iman M. Talaat
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Department of Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Haya Ibrahim
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Maha Saber-Ayad
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Department of Medical Pharmacology, College of Medicine, Cairo University, Cairo, Egypt
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Digre A, Lindskog C. The Human Protein Atlas-Spatial localization of the human proteome in health and disease. Protein Sci 2021; 30:218-233. [PMID: 33146890 PMCID: PMC7737765 DOI: 10.1002/pro.3987] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022]
Abstract
For a complete understanding of a system's processes and each protein's role in health and disease, it is essential to study protein expression with a spatial resolution, as the exact location of proteins at tissue, cellular, or subcellular levels is tightly linked to protein function. The Human Protein Atlas (HPA) project is a large-scale initiative aiming at mapping the entire human proteome using antibody-based proteomics and integration of various other omics technologies. The publicly available knowledge resource www.proteinatlas.org is one of the world's most visited biological databases and has been extensively updated during the last few years. The current version is divided into six main sections, each focusing on particular aspects of the human proteome: (a) the Tissue Atlas showing the distribution of proteins across all major tissues and organs in the human body; (b) the Cell Atlas showing the subcellular localization of proteins in single cells; (c) the Pathology Atlas showing the impact of protein levels on survival of patients with cancer; (d) the Blood Atlas showing the expression profiles of blood cells and actively secreted proteins; (e) the Brain Atlas showing the distribution of proteins in human, mouse, and pig brain; and (f) the Metabolic Atlas showing the involvement of proteins in human metabolism. The HPA constitutes an important resource for further understanding of human biology, and the publicly available datasets hold much promise for integration with other emerging efforts focusing on single cell analyses, both at transcriptomic and proteomic level.
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Affiliation(s)
- Andreas Digre
- Department of Immunology, Genetics and PathologyRudbeck Laboratory, Uppsala UniversityUppsalaSweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and PathologyRudbeck Laboratory, Uppsala UniversityUppsalaSweden
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Hamouche W, Bisserier M, Brojakowska A, Eskandari A, Fish K, Goukassian DA, Hadri L. Pathophysiology and pharmacological management of pulmonary and cardiovascular features of COVID-19. J Mol Cell Cardiol 2020; 153:72-85. [PMID: 33373644 PMCID: PMC7833205 DOI: 10.1016/j.yjmcc.2020.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/25/2020] [Accepted: 12/13/2020] [Indexed: 02/06/2023]
Abstract
The first confirmed case of novel Coronavirus Disease 2019 (COVID-19) in the United States was reported on January 20, 2020. As of November 24, 2020, close to 12.2 million cases of COVID-19 was confirmed in the US, with over 255,958 deaths. The rapid transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), its unusual and divergent presentation has strengthened the status of COVID-19 as a major public health threat. In this review, we aim to 1- discuss the epidemiological data from various COVID-19 patient cohorts around the world and the USA as well the associated risk factors; 2- summarize the pathophysiology of SARS-CoV-2 infection and the underlying molecular mechanisms for the respiratory and cardiovascular manifestations; 3- highlight the potential treatments and vaccines as well as current clinical trials for COVID-19.
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Affiliation(s)
- Walid Hamouche
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Internal Medicine Department, Brookdale University Hospital Medical Center, Brooklyn, NY, USA
| | - Malik Bisserier
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Agnieszka Brojakowska
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abrisham Eskandari
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kenneth Fish
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A Goukassian
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lahouaria Hadri
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Proteomic signatures of 16 major types of human cancer reveal universal and cancer-type-specific proteins for the identification of potential therapeutic targets. J Hematol Oncol 2020; 13:170. [PMID: 33287876 PMCID: PMC7720039 DOI: 10.1186/s13045-020-01013-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
Background Proteomic characterization of cancers is essential for a comprehensive understanding of key molecular aberrations. However, proteomic profiling of a large cohort of cancer tissues is often limited by the conventional approaches. Methods We present a proteomic landscape of 16 major types of human cancer, based on the analysis of 126 treatment-naïve primary tumor tissues, 94 tumor-matched normal adjacent tissues, and 12 normal tissues, using mass spectrometry-based data-independent acquisition approach.
Results In our study, a total of 8527 proteins were mapped to brain, head and neck, breast, lung (both small cell and non-small cell lung cancers), esophagus, stomach, pancreas, liver, colon, kidney, bladder, prostate, uterus and ovary cancers, including 2458 tissue-enriched proteins. Our DIA-based proteomic approach has characterized major human cancers and identified universally expressed proteins as well as tissue-type-specific and cancer-type-specific proteins. In addition, 1139 therapeutic targetable proteins and 21 cancer/testis (CT) antigens were observed. Conclusions Our discoveries not only advance our understanding of human cancers, but also have implications for the design of future large-scale cancer proteomic studies to assist the development of diagnostic and/or therapeutic targets in multiple cancers.
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Adam RS, van Neerven SM, Pleguezuelos-Manzano C, Simmini S, Léveillé N, de Groot NE, Holding AN, Markowetz F, Vermeulen L. Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development. Cancer Cell Int 2020; 20:578. [PMID: 33292279 PMCID: PMC7713000 DOI: 10.1186/s12935-020-01661-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 11/16/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cancer results from the accumulation of mutations leading to the acquisition of cancer promoting characteristics such as increased proliferation and resistance to cell death. In colorectal cancer, an early mutation leading to such features usually occurs in the APC or CTNNB1 genes, thereby activating Wnt signalling. However, substantial phenotypic differences between cancers originating within the same organ, such as molecular subtypes, are not fully reflected by differences in mutations. Indeed, the phenotype seems to result from a complex interplay between the cell-intrinsic features and the acquired mutations, which is difficult to disentangle when established tumours are studied. METHODS We use a 3D in vitro organoid model to study the early phase of colorectal cancer development. From three different murine intestinal locations we grow organoids. These are transformed to resemble adenomas after Wnt activation through lentiviral transduction with a stable form of β-Catenin. The gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing. To validate and generalize our findings, we use gene expression data from patients. RESULTS In reaction to Wnt activation we observe downregulation of location specific genes and differentiation markers. A similar effect is seen in patient data, where genes with significant differential expression between the normal left and right colon are downregulated in the cancer samples. Furthermore, the signature of Wnt target genes differs between the three intestinal locations in the organoids. The location specific Wnt signatures are dominated by genes which have been lowly expressed in the tissue of origin, and are the targets of transcription factors that are activated following enhanced Wnt signalling. CONCLUSION We observed that the region-specific cell identity has a substantial effect on the reaction to Wnt activation in a simple intestinal adenoma model. These findings provide a way forward in resolving the distinct biology between left- and right-sided human colon cancers with potential clinical relevance.
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Affiliation(s)
- Ronja S Adam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sanne M van Neerven
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Salvatore Simmini
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Research & Development Department at STEMCELL Technologies UK, 7100 Cambridge Research Park, Beach Drive Waterbeach, Cambridge, CB25 9TL, UK
| | - Nicolas Léveillé
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Nina E de Groot
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- The Alan Turing Institute, 96 Euston Road, Kings Cross, London, NW1 2DB, UK
- University of York, Wentworth Way, York, YO10 5DD, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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Zamorano Cuervo N, Grandvaux N. ACE2: Evidence of role as entry receptor for SARS-CoV-2 and implications in comorbidities. eLife 2020; 9:e61390. [PMID: 33164751 PMCID: PMC7652413 DOI: 10.7554/elife.61390] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus 19 disease (COVID-19) which presents a large spectrum of manifestations with fatal outcomes in vulnerable people over 70-years-old and with hypertension, diabetes, obesity, cardiovascular disease, COPD, and smoking status. Knowledge of the entry receptor is key to understand SARS-CoV-2 tropism, transmission and pathogenesis. Early evidence pointed to angiotensin-converting enzyme 2 (ACE2) as SARS-CoV-2 entry receptor. Here, we provide a critical summary of the current knowledge highlighting the limitations and remaining gaps that need to be addressed to fully characterize ACE2 function in SARS-CoV-2 infection and associated pathogenesis. We also discuss ACE2 expression and potential role in the context of comorbidities associated with poor COVID-19 outcomes. Finally, we discuss the potential co-receptors/attachment factors such as neuropilins, heparan sulfate and sialic acids and the putative alternative receptors, such as CD147 and GRP78.
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Affiliation(s)
| | - Nathalie Grandvaux
- CRCHUM - Centre Hospitalier de l’Université de MontréalQuébecCanada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de MontréalQuébecCanada
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Lewis MJ, Barnes MR, Blighe K, Goldmann K, Rana S, Hackney JA, Ramamoorthi N, John CR, Watson DS, Kummerfeld SK, Hands R, Riahi S, Rocher-Ros V, Rivellese F, Humby F, Kelly S, Bombardieri M, Ng N, DiCicco M, van der Heijde D, Landewé R, van der Helm-van Mil A, Cauli A, McInnes IB, Buckley CD, Choy E, Taylor PC, Townsend MJ, Pitzalis C. Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Rep 2020; 28:2455-2470.e5. [PMID: 31461658 PMCID: PMC6718830 DOI: 10.1016/j.celrep.2019.07.091] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/22/2019] [Accepted: 07/24/2019] [Indexed: 12/31/2022] Open
Abstract
There is a current imperative to unravel the hierarchy of molecular pathways that drive the transition of early to established disease in rheumatoid arthritis (RA). Herein, we report a comprehensive RNA sequencing analysis of the molecular pathways that drive early RA progression in the disease tissue (synovium), comparing matched peripheral blood RNA-seq in a large cohort of early treatment-naive patients, namely, the Pathobiology of Early Arthritis Cohort (PEAC). We developed a data exploration website (https://peac.hpc.qmul.ac.uk/) to dissect gene signatures across synovial and blood compartments, integrated with deep phenotypic profiling. We identified transcriptional subgroups in synovium linked to three distinct pathotypes: fibroblastic pauci-immune pathotype, macrophage-rich diffuse-myeloid pathotype, and a lympho-myeloid pathotype characterized by infiltration of lymphocytes and myeloid cells. This is suggestive of divergent pathogenic pathways or activation disease states. Pro-myeloid inflammatory synovial gene signatures correlated with clinical response to initial drug therapy, whereas plasma cell genes identified a poor prognosis subgroup with progressive structural damage. Deep phenotyping and RNA-seq of early rheumatoid arthritis individuals pre-treatment Synovial plasma cell gene expression predicts future progressive joint damage on X-ray Blood interferon gene signature associates with synovial B and plasma cell infiltration Interactive website enables RNA-seq and clinical data to be fully explored
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Affiliation(s)
- Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael R Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Alan Turing Institute, British Library, London NW1 2DB, UK
| | - Kevin Blighe
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Katriona Goldmann
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sharmila Rana
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jason A Hackney
- Bioinformatics and Computational Biology, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nandhini Ramamoorthi
- Biomarker Discovery OMNI, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher R John
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - David S Watson
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Alan Turing Institute, British Library, London NW1 2DB, UK; Oxford Internet Institute, University of Oxford, Oxford OX1 3JS, UK
| | - Sarah K Kummerfeld
- Bioinformatics and Computational Biology, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rebecca Hands
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sudeh Riahi
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Vidalba Rocher-Ros
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Felice Rivellese
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Frances Humby
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Stephen Kelly
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michele Bombardieri
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Nora Ng
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Maria DiCicco
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Robert Landewé
- Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, the Netherlands
| | | | - Alberto Cauli
- Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy
| | - Iain B McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Christopher D Buckley
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK; Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and the Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Ernest Choy
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Peter C Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and the Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Michael J Townsend
- Biomarker Discovery OMNI, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
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Xu T, Dong M, Wang Z, Li H, Li X. Elevated mRNA Expression Levels of NCAPG are Associated with Poor Prognosis in Ovarian Cancer. Cancer Manag Res 2020; 12:5773-5786. [PMID: 32765080 PMCID: PMC7369365 DOI: 10.2147/cmar.s253349] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Ovarian cancer is a major gynecologic malignancy that is often detected at a late stage due to the lack of detailed studies on its pathogenesis and reliable biomarkers for predicting its prognosis. MATERIALS AND METHODS Four ovarian cancer data sets GSE18520, GSE27651, GSE40595, and GSE52037 were downloaded from the Gene Expression Omnibus (GEO) database and the robust rank aggregation approach was used to find common differentially expressed genes (DEGs). Cytoscape software was used to construct and detect key models of protein-protein interaction (PPI) network. While the expression, prognostic value and potential mechanism of the hub gene non-SMC condensin I complex subunit G (NCAPG) was carried out through Gene Expression Profiling Interactive Analysis, Kaplan-Meier plotter online dataset and gene set enrichment analysis. To further investigate the role of NCAPG in ovarian cancer, in vitro experiments were carried out. RESULTS A total of 232 DEGs were identified in the four GEO datasets; and we detected 32 hub genes from the PPI network and 21 of these genes were associated with ovarian cancer prognosis, one of which was NCAPG. NCAPG was significantly upregulated in most of the ovarian cancer samples. High NCAPG expression was mainly involved in homologous recombination, DNA replication, proteasome, and more correlated pathways. NCAPG knockdown arrested the cell cycle, inhibited the proliferation, and attenuated the migration ability of A2780 cells. Meanwhile, silencing of NCAPG significantly promoted cisplatin-induced apoptosis thus increased the sensitivity to cisplatin. CONCLUSION NCAPG together with the other 31 hub genes play a vital role in the tumorigenesis of ovarian, meanwhile, the cell cycle pathway may be a potential pathway contributing to progression in OC; and NCAPG expression can be used as a promising target for the treatment of OC.
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Affiliation(s)
- Tao Xu
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of HUST, Wuhan, Hubei430030, People’s Republic of China
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College of HUST, Wuhan, Hubei430030, People’s Republic of China
| | - Menglu Dong
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of HUST, Wuhan, Hubei430030, People’s Republic of China
| | - Zhi Wang
- Department of Obstetrics and Gynecology, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College of HUST, Wuhan, Hubei430030, People’s Republic of China
| | - Hanning Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of HUST, Wuhan, Hubei430030, People’s Republic of China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of HUST, Wuhan, Hubei430030, People’s Republic of China
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50
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Hikmet F, Méar L, Edvinsson Å, Micke P, Uhlén M, Lindskog C. The protein expression profile of ACE2 in human tissues. Mol Syst Biol 2020; 16:e9610. [PMID: 32715618 PMCID: PMC7383091 DOI: 10.15252/msb.20209610] [Citation(s) in RCA: 661] [Impact Index Per Article: 165.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 01/08/2023] Open
Abstract
The novel SARS-coronavirus 2 (SARS-CoV-2) poses a global challenge on healthcare and society. For understanding the susceptibility for SARS-CoV-2 infection, the cell type-specific expression of the host cell surface receptor is necessary. The key protein suggested to be involved in host cell entry is angiotensin I converting enzyme 2 (ACE2). Here, we report the expression pattern of ACE2 across > 150 different cell types corresponding to all major human tissues and organs based on stringent immunohistochemical analysis. The results were compared with several datasets both on the mRNA and protein level. ACE2 expression was mainly observed in enterocytes, renal tubules, gallbladder, cardiomyocytes, male reproductive cells, placental trophoblasts, ductal cells, eye, and vasculature. In the respiratory system, the expression was limited, with no or only low expression in a subset of cells in a few individuals, observed by one antibody only. Our data constitute an important resource for further studies on SARS-CoV-2 host cell entry, in order to understand the biology of the disease and to aid in the development of effective treatments to the viral infection.
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Affiliation(s)
- Feria Hikmet
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Loren Méar
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Åsa Edvinsson
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Patrick Micke
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Mathias Uhlén
- Science for Life LaboratorySchool of Engineering Sciences in Chemistry, Biotechnology and HealthKTH ‐ Royal Institute of TechnologyStockholmSweden
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | - Cecilia Lindskog
- Rudbeck LaboratoryDepartment of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
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