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Picard M, Scott-Boyer MP, Bodein A, Leclercq M, Prunier J, Périn O, Droit A. Target repositioning using multi-layer networks and machine learning: The case of prostate cancer. Comput Struct Biotechnol J 2024; 24:464-475. [PMID: 38983753 PMCID: PMC11231507 DOI: 10.1016/j.csbj.2024.06.012] [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: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
The discovery of novel therapeutic targets, defined as proteins which drugs can interact with to induce therapeutic benefits, typically represent the first and most important step of drug discovery. One solution for target discovery is target repositioning, a strategy which relies on the repurposing of known targets for new diseases, leading to new treatments, less side effects and potential drug synergies. Biological networks have emerged as powerful tools for integrating heterogeneous data and facilitating the prediction of biological or therapeutic properties. Consequently, they are widely employed to predict new therapeutic targets by characterizing potential candidates, often based on their interactions within a Protein-Protein Interaction (PPI) network, and their proximity to genes associated with the disease. However, over-reliance on PPI networks and the assumption that potential targets are necessarily near known genes can introduce biases that may limit the effectiveness of these methods. This study addresses these limitations in two ways. First, by exploiting a multi-layer network which incorporates additional information such as gene regulation, metabolite interactions, metabolic pathways, and several disease signatures such as Differentially Expressed Genes, mutated genes, Copy Number Alteration, and structural variants. Second, by extracting relevant features from the network using several approaches including proximity to disease-associated genes, but also unbiased approaches such as propagation-based methods, topological metrics, and module detection algorithms. Using prostate cancer as a case study, the best features were identified and utilized to train machine learning algorithms to predict 5 novel promising therapeutic targets for prostate cancer: IGF2R, C5AR, RAB7, SETD2 and NPBWR1.
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Affiliation(s)
- Milan Picard
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Julien Prunier
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Transformation and Innovation Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
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2
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Ramesh J, Gopalakrishnan RM, Nguyen THA, Lai SK, Li HY, Kim PS, Kutzner A, Inoue N, Heese K. Deciphering the molecular landscape of the FAM72 gene family: Implications for stem cell biology and cancer. Neurochem Int 2024; 180:105853. [PMID: 39236808 DOI: 10.1016/j.neuint.2024.105853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/07/2024]
Abstract
Family with sequence similarity 72 (FAM72) is a protein-coding gene family located on chromosome 1 in humans, uniquely featuring four paralogs: FAM72A, FAM72B, FAM72C, and FAM72D. While FAM72's presence as a gene pair with the SLIT-ROBO Rho GTPase-activating protein 2 (SRGAP2) is intriguing, its functional roles, particularly in neural stem cells, remain incompletely understood. This review explores the distinct characteristics of FAM72, shedding light on its expression patterns, potential roles in cell cycle regulation, stem cell renewal and implications in neurogenesis and tumorigenesis.
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Affiliation(s)
- Janani Ramesh
- Department of Medical Biochemistry, Dr ALM Postgraduate Institute of Biomedical Sciences, University of Madras, Chennai, Tamil Nadu, 600-113, India.
| | - Raja Mohan Gopalakrishnan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu, 600-025, India.
| | - Tuan Hoang Anh Nguyen
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
| | - Soak-Kuan Lai
- School of Biological Sciences, College of Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637-551, Singapore.
| | - Hoi-Yeung Li
- School of Biological Sciences, College of Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637-551, Singapore.
| | - Pok-Son Kim
- Department of Information Security, Cryptology, and Mathematics, Kookmin University, Seoul, 136-702, Republic of Korea.
| | - Arne Kutzner
- Department of Information Systems, College of Computer Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
| | - Noriko Inoue
- Osaka University Institute for Sports and Global Health, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
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3
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Silva EFP, Gaia RC, Mulim HA, Pinto LFB, Iung LHS, Brito LF, Pedrosa VB. Genome-Wide Association Study of Conformation Traits in Brazilian Holstein Cattle. Animals (Basel) 2024; 14:2472. [PMID: 39272257 PMCID: PMC11394126 DOI: 10.3390/ani14172472] [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: 07/18/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
The linear conformation of animals exerts an influence on health, reproduction, production, and welfare, in addition to longevity, which directly affects the profitability of milk-producing farms. The objectives of this study were (1) to perform genome-wide association studies (GWASs) of conformation traits, namely the Rump, Feet and Legs, Mammary System, Dairy Strength, and Final Classification traits, and (2) to identify genes and related pathways involved in physiological processes associated with conformation traits in Brazilian Holstein cattle. Phenotypic and genotypic data from 2339 Holstein animals distributed across the states of Rio Grande do Sul, Paraná, São Paulo, and Minas Gerais were used. The genotypic data were obtained with a 100 K SNP marker panel. The single-step genome-wide association study (ssGWAS) method was employed in the analyses. Genes close to a significant SNP were identified in an interval of 100 kb up- and downstream using the Ensembl database available in the BioMart tool. The DAVID database was used to identify the main metabolic pathways and the STRING program was employed to create the gene regulatory network. In total, 36 significant SNPs were found on 15 chromosomes; 27 of these SNPs were linked to genes that may influence the traits studied. Fourteen genes most closely related to the studied traits were identified, as well as four genes that showed interactions in important metabolic pathways such as myogenesis, adipogenesis, and angiogenesis. Among the total genes, four were associated with myogenesis (TMOD2, TMOD3, CCND2, and CTBP2), three with angiogenesis (FGF23, FGF1, and SCG3), and four with adipogenesis and body size and development (C5H12orf4, CCND2, EMILIN1, and FGF6). These results contribute to a better understanding of the biological mechanisms underlying phenotypic variability in conformation traits in Brazilian Holstein cattle.
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Affiliation(s)
- Emanueli F P Silva
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84010-330, PR, Brazil
| | - Rita C Gaia
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84010-330, PR, Brazil
| | - Henrique A Mulim
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Laiza H S Iung
- Neogen Corporation, Pindamonhangaba 12412-800, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Victor B Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84010-330, PR, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Neogen Corporation, Biotechnology Research, Lincoln, NE 68504, USA
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4
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Huang D, Jiao X, Huang S, Liu J, Si H, Qi D, Pei X, Lu D, Wang Y, Li Z. Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing. Ocul Surf 2024; 34:60-95. [PMID: 38945476 DOI: 10.1016/j.jtos.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE The lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting an aqueous layer of the tear film. However, a healthy lacrimal gland's inventory of cell types and heterogeneity remains understudied. METHODS Here, 10X Genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 43,850 high-quality cells, we produced an atlas of cell heterogeneity and defined cell types using classic marker genes. The possible functions of these cells were analyzed through bioinformatics analysis. Additionally, the CellChat was employed for a preliminary analysis of the cell-cell communication network in the ELG. RESULTS Over 37 subclasses of cells were identified, including seven types of glandular epithelial cells, three types of fibroblasts, ten types of myeloid-derived immune cells, at least eleven types of lymphoid-derived immune cells, and five types of vascular-associated cell subsets. The cell-cell communication network analysis revealed that fibroblasts and immune cells play a pivotal role in the dense intercellular communication network within the mouse ELG. CONCLUSIONS This study provides a comprehensive transcriptome atlas and related database of the mouse ELG.
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Affiliation(s)
- Duliurui Huang
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xinwei Jiao
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Shenzhen Huang
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Jiangman Liu
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hongli Si
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Di Qi
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Xiaoting Pei
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Dingli Lu
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China
| | - Yimian Wang
- Division of Medicine, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Zhijie Li
- Department of Ophthalmology, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, Henan, China; Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450000, China.
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5
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O'Brien CL, Summers KM, Martin NM, Carter-Cusack D, Yang Y, Barua R, Dixit OVA, Hume DA, Pavli P. The relationship between extreme inter-individual variation in macrophage gene expression and genetic susceptibility to inflammatory bowel disease. Hum Genet 2024; 143:233-261. [PMID: 38421405 PMCID: PMC11043138 DOI: 10.1007/s00439-024-02642-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024]
Abstract
The differentiation of resident intestinal macrophages from blood monocytes depends upon signals from the macrophage colony-stimulating factor receptor (CSF1R). Analysis of genome-wide association studies (GWAS) indicates that dysregulation of macrophage differentiation and response to microorganisms contributes to susceptibility to chronic inflammatory bowel disease (IBD). Here, we analyzed transcriptomic variation in monocyte-derived macrophages (MDM) from affected and unaffected sib pairs/trios from 22 IBD families and 6 healthy controls. Transcriptional network analysis of the data revealed no overall or inter-sib distinction between affected and unaffected individuals in basal gene expression or the temporal response to lipopolysaccharide (LPS). However, the basal or LPS-inducible expression of individual genes varied independently by as much as 100-fold between subjects. Extreme independent variation in the expression of pairs of HLA-associated transcripts (HLA-B/C, HLA-A/F and HLA-DRB1/DRB5) in macrophages was associated with HLA genotype. Correlation analysis indicated the downstream impacts of variation in the immediate early response to LPS. For example, variation in early expression of IL1B was significantly associated with local SNV genotype and with subsequent peak expression of target genes including IL23A, CXCL1, CXCL3, CXCL8 and NLRP3. Similarly, variation in early IFNB1 expression was correlated with subsequent expression of IFN target genes. Our results support the view that gene-specific dysregulation in macrophage adaptation to the intestinal milieu is associated with genetic susceptibility to IBD.
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Affiliation(s)
- Claire L O'Brien
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Natalia M Martin
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Yuanhao Yang
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Rasel Barua
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia
| | - Ojas V A Dixit
- Centre for Research in Therapeutics Solutions, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia.
| | - Paul Pavli
- Inflammatory Bowel Disease Research Group, Canberra Hospital, Canberra, ACT, Australia.
- School of Medicine and Psychology, College of Health and Medicine, Australian National University, Canberra, ACT, Australia.
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6
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Wu Z, Shih B, Macdonald J, Meunier D, Hogan K, Chintoan-Uta C, Gilhooley H, Hu T, Beltran M, Henderson NC, Sang HM, Stevens MP, McGrew MJ, Balic A. Development and function of chicken XCR1 + conventional dendritic cells. Front Immunol 2023; 14:1273661. [PMID: 37954617 PMCID: PMC10634274 DOI: 10.3389/fimmu.2023.1273661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
Conventional dendritic cells (cDCs) are antigen-presenting cells (APCs) that play a central role in linking innate and adaptive immunity. cDCs have been well described in a number of different mammalian species, but remain poorly characterised in the chicken. In this study, we use previously described chicken cDC specific reagents, a novel gene-edited chicken line and single-cell RNA sequencing (scRNAseq) to characterise chicken splenic cDCs. In contrast to mammals, scRNAseq analysis indicates that the chicken spleen contains a single, chemokine receptor XCR1 expressing, cDC subset. By sexual maturity the XCR1+ cDC population is the most abundant mononuclear phagocyte cell subset in the chicken spleen. scRNAseq analysis revealed substantial heterogeneity within the chicken splenic XCR1+ cDC population. Immature MHC class II (MHCII)LOW XCR1+ cDCs expressed a range of viral resistance genes. Maturation to MHCIIHIGH XCR1+ cDCs was associated with reduced expression of anti-viral gene expression and increased expression of genes related to antigen presentation via the MHCII and cross-presentation pathways. To visualise and transiently ablate chicken XCR1+ cDCs in situ, we generated XCR1-iCaspase9-RFP chickens using a CRISPR-Cas9 knockin transgenesis approach to precisely edit the XCR1 locus, replacing the XCR1 coding region with genes for a fluorescent protein (TagRFP), and inducible Caspase 9. After inducible ablation, the chicken spleen is initially repopulated by immature CD1.1+ XCR1+ cDCs. XCR1+ cDCs are abundant in the splenic red pulp, in close association with CD8+ T-cells. Knockout of XCR1 prevented this clustering of cDCs with CD8+ T-cells. Taken together these data indicate a conserved role for chicken and mammalian XCR1+ cDCs in driving CD8+ T-cells responses.
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Affiliation(s)
- Zhiguang Wu
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Barbara Shih
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Joni Macdonald
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Dominique Meunier
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Kris Hogan
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | | | - Hazel Gilhooley
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Tuanjun Hu
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Mariana Beltran
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C. Henderson
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council (MRC) Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Helen M. Sang
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Mark P. Stevens
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Michael J. McGrew
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Adam Balic
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
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7
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Oleksiewicz U, Machnik M, Sobocińska J, Molenda S, Olechnowicz A, Florczak A, Smolibowski M, Kaczmarek M. ZNF714 Supports Pro-Oncogenic Features in Lung Cancer Cells. Int J Mol Sci 2023; 24:15530. [PMID: 37958512 PMCID: PMC10649060 DOI: 10.3390/ijms242115530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/10/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
Despite the ongoing progress in diagnosis and treatments, cancer remains a threat to more than one-third of the human population. The emerging data indicate that many Krüppel-associated box zinc finger proteins (KRAB-ZNF) belonging to a large gene family may be involved in carcinogenesis. Our previous study identified Zinc Finger Protein 714 (ZNF714), a KRAB-ZNF gene of unknown function, as being commonly overexpressed in many tumors, pointing to its hypothetical oncogenic role. Here, we harnessed The Cancer Genome Atlas (TCGA)-centered databases and performed functional studies with transcriptomic and methylomic profiling to explore ZNF714 function in cancer. Our pan-cancer analyses confirmed frequent ZNF714 overexpression in multiple tumors, possibly due to regional amplification, promoter hypomethylation, and Nuclear Transcription Factor Y Subunit Beta (NFYB) signaling. We also showed that ZNF714 expression correlates with tumor immunosuppressive features. The in vitro studies indicated that ZNF714 expression positively associates with proliferation, migration, and invasion. The transcriptomic analysis of ZNF714 knocked-down cells demonstrated deregulation of cell adhesion, migration, proliferation, apoptosis, and differentiation. Importantly, we provided evidence that ZNF714 negatively regulates the expression of several known TSGs indirectly via promoter methylation. However, as ZNF714 did not show nuclear localization in our research model, the regulatory mechanisms exerted by ZNF714 require further investigation. In conclusion, our results reveal, for the first time, that ZNF714 may support pro-oncogenic features in lung cancer cells.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Swiecickiego 6 Street, 60-781 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
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8
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Okafor AE, Lin X, Situ C, Wei X, Xiang Y, Wei X, Wu Z, Diao Y. Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state. J Cell Biol 2023; 222:e202211073. [PMID: 37382627 PMCID: PMC10309185 DOI: 10.1083/jcb.202211073] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/30/2023] [Accepted: 05/17/2023] [Indexed: 06/30/2023] Open
Abstract
A balance between self-renewal and differentiation is critical for the regenerative capacity of tissue-resident stem cells. In skeletal muscle, successful regeneration requires the orchestrated activation, proliferation, and differentiation of muscle satellite cells (MuSCs) that are normally quiescent. A subset of MuSCs undergoes self-renewal to replenish the stem cell pool, but the features that identify and define self-renewing MuSCs remain to be elucidated. Here, through single-cell chromatin accessibility analysis, we reveal the self-renewal versus differentiation trajectories of MuSCs over the course of regeneration in vivo. We identify Betaglycan as a unique marker of self-renewing MuSCs that can be purified and efficiently contributes to regeneration after transplantation. We also show that SMAD4 and downstream genes are genetically required for self-renewal in vivo by restricting differentiation. Our study unveils the identity and mechanisms of self-renewing MuSCs, while providing a key resource for comprehensive analysis of muscle regeneration.
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Affiliation(s)
- Arinze E. Okafor
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Xin Lin
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Chenghao Situ
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xiaolin Wei
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
| | - Xiuqing Wei
- Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Zhenguo Wu
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
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9
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Xu Y, Zhang T, Zhou Q, Hu M, Qi Y, Xue Y, Nie Y, Wang L, Bao Z, Shi W. A single-cell transcriptome atlas profiles early organogenesis in human embryos. Nat Cell Biol 2023; 25:604-615. [PMID: 36928764 DOI: 10.1038/s41556-023-01108-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4-6 week human embryos when essentially all organs are just laid out. On the basis of over 180,000 single-cell transcriptomes, we generated a comprehensive atlas of 313 clusters in 18 developmental systems, which were annotated with a collection of ontology and markers from 157 publications. Together with spatial transcriptome on embryonic sections, we characterized the molecule and spatial architecture of previously unappreciated cell types. Combined with data from other vertebrates, the rich information shed light on spatial patterning of axes, systemic temporal regulation of developmental progression and potential human-specific regulation. Our study provides a compendium of early progenitor cells of human organs, which can serve as the root of lineage analysis in organogenesis.
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Affiliation(s)
- Yichi Xu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Tengjiao Zhang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qin Zhou
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Mengzhu Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yao Qi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yifang Xue
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Yuxiao Nie
- School of Pharmacy, Fudan University, Shanghai, China
| | - Lihui Wang
- Traditional Chinese Medicine Hospital of Kunshan, Suzhou, China
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
| | - Weiyang Shi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
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10
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Winnard PT, Morsberger L, Yonescu R, Jiang L, Zou YS, Raman V. Isogenic Cell Lines Derived from Specific Organ Metastases Exhibit Divergent Cytogenomic Aberrations. Cancers (Basel) 2023; 15:cancers15051420. [PMID: 36900209 PMCID: PMC10000985 DOI: 10.3390/cancers15051420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023] Open
Abstract
Aneuploidy, a deviation in chromosome numbers from the normal diploid set, is now recognized as a fundamental characteristic of all cancer types and is found in 70-90% of all solid tumors. The majority of aneuploidies are generated by chromosomal instability (CIN). CIN/aneuploidy is an independent prognostic marker of cancer survival and is a cause of drug resistance. Hence, ongoing research has been directed towards the development of therapeutics aimed at targeting CIN/aneuploidy. However, there are relatively limited reports on the evolution of CIN/aneuploidies within or across metastatic lesions. In this work, we built on our previous studies using a human xenograft model system of metastatic disease in mice that is based on isogenic cell lines derived from the primary tumor and specific metastatic organs (brain, liver, lung, and spine). As such, these studies were aimed at exploring distinctions and commonalities between the karyotypes; biological processes that have been implicated in CIN; single-nucleotide polymorphisms (SNPs); losses, gains, and amplifications of chromosomal regions; and gene mutation variants across these cell lines. Substantial amounts of inter- and intra-heterogeneity were found across karyotypes, along with distinctions between SNP frequencies across each chromosome of each metastatic cell line relative the primary tumor cell line. There were disconnects between chromosomal gains or amplifications and protein levels of the genes in those regions. However, commonalities across all cell lines provide opportunities to select biological processes as druggable targets that could have efficacy against the primary tumor, as well as metastases.
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Affiliation(s)
- Paul T. Winnard
- Department of Radiology and Radiological Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Laura Morsberger
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Raluca Yonescu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Liqun Jiang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ying S. Zou
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Correspondence: (Y.S.Z.); (V.R.); Tel.: +1-410-955-7492 (V.R.); Fax: +1-410-955-0484 (V.R.)
| | - Venu Raman
- Department of Radiology and Radiological Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence: (Y.S.Z.); (V.R.); Tel.: +1-410-955-7492 (V.R.); Fax: +1-410-955-0484 (V.R.)
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11
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In vivo and in vitro matured bovine oocytes present a distinct pattern of single-cell gene expression. ZYGOTE 2023; 31:31-43. [PMID: 36263617 DOI: 10.1017/s0967199422000478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Oocyte gene expression is a well controlled event that promotes gamete competence to undergo maturation, fertilization, and to support early embryo development, directly affecting reproductive outcomes. Considering that in vivo controlled ovarian stimulation or in vitro maturation (IVM) for the acquisition of mature oocytes has distinct implications for gene expression, we sought to evaluate the effects of these procedures on the expression of competence-related genes in single-cell oocytes. Healthy Nelore cows of reproductive age were synchronized to harvest in vivo matured oocytes; ovaries from slaughtered animals were used to obtain cumulus-oocyte complexes that were in vitro matured. Single-cell gene expression was performed using TaqMan Low-Density Arrays and 42 genes were evaluated. In silico analysis of protein interactions and Gene Ontology (GO) analysis was performed. Reduced gene expression was observed for 24 targets in IVM oocytes when compared with those of in vivo matured oocytes (P < 0.05). Differences ranged from 1.5-fold to 4.8-fold higher in in vivo oocytes and the BMP15 (5.28), GDF9 (6.23), NOBOX (7.25), HSPA8 (7.85) and MSX1 (11.00) showed the greatest fold increases. The strongest score of functional interactions was observed between the CDC20 and CKS2, with the differentially expressed gene CDC20 being the main marker behind GO enrichment. IVM negatively affected the expression of important genes related to oocyte competency, and showed higher expression levels in in vivo matured oocytes. In vivo controlled ovarian stimulation may be a better strategy to achieve proper oocyte competence and increase the success of assisted reproductive technologies.
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12
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Zhao Y, Zhang L, Hu Q, Zhu D, Xie Z. Identification and analysis of C17orf53 as a prognostic signature for hepatocellular carcinoma. Comput Biol Med 2023; 152:106348. [PMID: 36470143 DOI: 10.1016/j.compbiomed.2022.106348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/28/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
C17orf53 is a novel gene for DNA synthesis and homologous recombination. However, the exact role of C17orf53 in hepatocellular carcinoma (HCC) remains unclear. In this study, we analyzed it using a set of public datasets. UALCAN, Human Protein Atlas (HPA), Kaplan‒Meier Plotter, Tumor Immune Estimation Resource (TIMER), cBioPortal, GEPIA, GeneMANIA, and LinkedOmics were used. Functional analysis was conducted in SK-Hep-1 cells by using small interfering RNA (siRNA). C17orf53 was highly expressed and predicted unfavorable survival in HCC patients. Moreover, it showed positive correlations with the abundance of B cells, macrophages and dendritic cells. In addition, we identified 126 genes that were positively correlated with C17orf53 and its coeffector minichromosome maintenance 8 (MCM8). These genes were mainly enriched in the cell cycle, DNA replication and Fanconi anemia pathways. Knockdown of C17orf53 significantly inhibited the proliferation of SK-Hep-1 cells and decreased the expression of MCM8, cyclin D1 and proliferating cell nuclear antigen (PCNA). Overall, C17orf53 is a novel prognostic signature for HCC.
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Affiliation(s)
- Yalei Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lingjian Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qingqing Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhongyang Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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13
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Ma C, Li C, Ma H, Yu D, Zhang Y, Zhang D, Su T, Wu J, Wang X, Zhang L, Chen CL, Zhang YE. Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum. Genome Biol 2022; 23:251. [PMID: 36474250 PMCID: PMC9724437 DOI: 10.1186/s13059-022-02821-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of cancer. The antagonistic pleiotropy hypothesis predicts that primate-specific genes (PSGs) tend to promote tumorigenesis, while the molecular atavism hypothesis predicts that PSGs involved in tumors may represent recently derived duplicates of unicellular genes. However, these predictions have not been tested. RESULTS By taking advantage of pan-cancer genomic data, we find the upregulation of PSGs across 13 cancer types, which is facilitated by copy-number gain and promoter hypomethylation. Meta-analyses indicate that upregulated PSGs (uPSGs) tend to promote tumorigenesis and to play cell cycle-related roles. The cell cycle-related uPSGs predominantly represent derived duplicates of unicellular genes. We prioritize 15 uPSGs and perform an in-depth analysis of one unicellular gene-derived duplicate involved in the cell cycle, DDX11. Genome-wide screening data and knockdown experiments demonstrate that DDX11 is broadly essential across cancer cell lines. Importantly, non-neutral amino acid substitution patterns and increased expression indicate that DDX11 has been under positive selection. Finally, we find that cell cycle-related uPSGs are also preferentially upregulated in the highly proliferative embryonic cerebrum. CONCLUSIONS Consistent with the predictions of the atavism and antagonistic pleiotropy hypotheses, primate-specific genes, especially those PSGs derived from cell cycle-related genes that emerged in unicellular ancestors, contribute to the early proliferation of the human cerebrum at the cost of hitchhiking by similarly highly proliferative cancer cells.
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Affiliation(s)
- Chenyu Ma
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Li
- School of Engineering Medicine, Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), and Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufei Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Dan Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianhan Su
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianmin Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005, Paris, France
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Chinese Institute for Brain Research, Beijing, 102206, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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14
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Wiarda JE, Trachsel JM, Sivasankaran SK, Tuggle CK, Loving CL. Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells. Life Sci Alliance 2022; 5:e202201442. [PMID: 35995567 PMCID: PMC9396248 DOI: 10.26508/lsa.202201442] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 12/13/2022] Open
Abstract
Lymphocytes can heavily influence intestinal health, but resolving intestinal lymphocyte function is challenging as the intestine contains a vastly heterogeneous mixture of cells. Pigs are an advantageous biomedical model, but deeper understanding of intestinal lymphocytes is warranted to improve model utility. Twenty-six cell types were identified in the porcine ileum by single-cell RNA sequencing and further compared with cells in human and murine ileum. Though general consensus of cell subsets across species was revealed, some porcine-specific lymphocyte subsets were identified. Differential tissue dissection and in situ analyses conferred spatial context, revealing similar locations of lymphocyte subsets in Peyer's patches and epithelium in pig-to-human comparisons. Like humans, activated and effector lymphocytes were abundant in the ileum but not periphery of pigs, suggesting tissue-specific and/or activation-associated gene expression. Gene signatures for peripheral and ileal innate lymphoid cells newly discovered in pigs were defined and highlighted similarities to human innate lymphoid cells. Overall, we reveal novel lymphocyte subsets in pigs and highlight utility of pigs for intestinal research applications.
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Affiliation(s)
- Jayne E Wiarda
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
- Immunobiology Graduate Program, Iowa State University, Ames, IA, USA
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, USA
| | - Julian M Trachsel
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Sathesh K Sivasankaran
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
- Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | | | - Crystal L Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
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15
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Ehnes DD, Alghadeer A, Hanson-Drury S, Zhao YT, Tilmes G, Mathieu J, Ruohola-Baker H. Sci-Seq of Human Fetal Salivary Tissue Introduces Human Transcriptional Paradigms and a Novel Cell Population. FRONTIERS IN DENTAL MEDICINE 2022; 3:887057. [PMID: 36540608 PMCID: PMC9762771 DOI: 10.3389/fdmed.2022.887057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
Multiple pathologies and non-pathological factors can disrupt the function of the non-regenerative human salivary gland including cancer and cancer therapeutics, autoimmune diseases, infections, pharmaceutical side effects, and traumatic injury. Despite the wide range of pathologies, no therapeutic or regenerative approaches exist to address salivary gland loss, likely due to significant gaps in our understanding of salivary gland development. Moreover, identifying the tissue of origin when diagnosing salivary carcinomas requires an understanding of human fetal development. Using computational tools, we identify developmental branchpoints, a novel stem cell-like population, and key signaling pathways in the human developing salivary glands by analyzing our human fetal single-cell sequencing data. Trajectory and transcriptional analysis suggest that the earliest progenitors yield excretory duct and myoepithelial cells and a transitional population that will yield later ductal cell types. Importantly, this single-cell analysis revealed a previously undescribed population of stem cell-like cells that are derived from SD and expresses high levels of genes associated with stem cell-like function. We have observed these rare cells, not in a single niche location but dispersed within the developing duct at later developmental stages. Our studies introduce new human-specific developmental paradigms for the salivary gland and lay the groundwork for the development of translational human therapeutics.
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Affiliation(s)
- Devon Duron Ehnes
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Ammar Alghadeer
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Sesha Hanson-Drury
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
| | - Yan Ting Zhao
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
| | - Gwen Tilmes
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Julie Mathieu
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Hannele Ruohola-Baker
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
- Department of Bioengineering, University of Washington, Seattle, WA, United States
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16
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Tan Y, Flynn WF, Sivajothi S, Luo D, Bozal SB, Davé M, Luciano AA, Robson P, Luciano DE, Courtois ET. Single-cell analysis of endometriosis reveals a coordinated transcriptional programme driving immunotolerance and angiogenesis across eutopic and ectopic tissues. Nat Cell Biol 2022; 24:1306-1318. [PMID: 35864314 PMCID: PMC9901845 DOI: 10.1038/s41556-022-00961-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/09/2022] [Indexed: 02/08/2023]
Abstract
Endometriosis is characterized by the growth of endometrial-like tissue outside the uterus. It affects many women during their reproductive age, causing years of pelvic pain and potential infertility. Its pathophysiology remains largely unknown, which limits early diagnosis and treatment. We characterized peritoneal and ovarian lesions at single-cell transcriptome resolution and compared them to matched eutopic endometrium, unaffected endometrium and organoids derived from these tissues, generating data on over 122,000 cells across 14 individuals. We spatially localized many of the cell types using imaging mass cytometry. We identify a perivascular mural cell specific to the peritoneal lesions, with dual roles in angiogenesis promotion and immune cell trafficking. We define an immunotolerant peritoneal niche, fundamental differences in eutopic endometrium and between lesion microenvironments and an unreported progenitor-like epithelial cell subpopulation. Altogether, this study provides a holistic view of the endometriosis microenvironment that represents a comprehensive cell atlas of the disease in individuals undergoing hormonal treatment, providing essential information for future therapeutics and diagnostics.
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Affiliation(s)
- Yuliana Tan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - William F Flynn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Diane Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Suleyman B Bozal
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Monica Davé
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Anthony A Luciano
- Department of Obstetrics and Gynecology, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
| | - Danielle E Luciano
- Department of Obstetrics and Gynecology, University of Connecticut School of Medicine, Farmington, CT, USA.
| | - Elise T Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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17
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Theilgaard-Mönch K, Pundhir S, Reckzeh K, Su J, Tapia M, Furtwängler B, Jendholm J, Jakobsen JS, Hasemann MS, Knudsen KJ, Cowland JB, Fossum A, Schoof E, Schuster MB, Porse BT. Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation : In memoriam Professor Niels Borregaard. Nat Commun 2022; 13:3595. [PMID: 35739121 PMCID: PMC9225994 DOI: 10.1038/s41467-022-31332-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/14/2022] [Indexed: 12/14/2022] Open
Abstract
Differentiation of multipotent stem cells into mature cells is fundamental for development and homeostasis of mammalian tissues, and requires the coordinated induction of lineage-specific transcriptional programs and cell cycle withdrawal. To understand the underlying regulatory mechanisms of this fundamental process, we investigated how the tissue-specific transcription factors, CEBPA and CEBPE, coordinate cell cycle exit and lineage-specification in vivo during granulocytic differentiation. We demonstrate that CEBPA promotes lineage-specification by launching an enhancer-primed differentiation program and direct activation of CEBPE expression. Subsequently, CEBPE confers promoter-driven cell cycle exit by sequential repression of MYC target gene expression at the G1/S transition and E2F-meditated G2/M gene expression, as well as by the up-regulation of Cdk1/2/4 inhibitors. Following cell cycle exit, CEBPE unleashes the CEBPA-primed differentiation program to generate mature granulocytes. These findings highlight how tissue-specific transcription factors coordinate cell cycle exit with differentiation through the use of distinct gene regulatory elements.
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Affiliation(s)
- Kim Theilgaard-Mönch
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark.
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Reckzeh
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jinyu Su
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marta Tapia
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin Furtwängler
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johan Jendholm
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Janus Schou Jakobsen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie Sigurd Hasemann
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Jermiin Knudsen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jack Bernard Cowland
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Anna Fossum
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erwin Schoof
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Mikkel Bruhn Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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18
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Li X, Chen X, Yuan Y, Zhai R, Cho WC, Jiang X. Identifying Immune Cell Infiltration and Effective Diagnostic Biomarkers in Lung Adenocarcinoma by Comprehensive Bioinformatics Analysis and In Vitro Study. Front Oncol 2022; 12:916947. [PMID: 35707363 PMCID: PMC9189382 DOI: 10.3389/fonc.2022.916947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Family with sequence similarity 72B (FAM72B) has been characterized in the regulation of neuronal development. Nevertheless, the prognostic value of FAM72B expression and its function in the immune microenvironment of lung adenocarcinoma (LUAD) currently remains elusive. In this study, by adopting bioinformatics methodology and experimental verification, we found that FAM72B was upregulated in lung cancer tissues and cell lines, and a higher FAM72B level predicted an unfavorable clinical outcome in LUAD patients. The knockdown of FAM72B significantly inhibited cell proliferation, cell migration, and induced cell apoptosis in LUAD. The receiver operating characteristic curve suggested that FAM72B had a high predictive accuracy for the outcomes of LUAD. Kyoto Encyclopedia of Genes and Genomes and Gene Set Enrichment Analyses confirmed that FAM72B-related genes were involved in cell proliferation and immune-response signaling pathway. Moreover, upregulated FAM72B expression was significantly associated with immune cell infiltration in the LUAD tumor microenvironment. Meanwhile, a potential ceRNA network was constructed to identify the lncRNA-AL360270.2/TMPO-AS1/AC125807.2/has-let-7a/7b/7c/7e/7f/FAM72B regulatory axis that regulates FAM72B overexpression in LUAD and is associated with a poor prognosis. We also confirmed that AL360270.2, TMPO-AS1, and AC125807.2 were significantly upregulated in LUAD cell lines than in human bronchial epithelial cells. In conclusion, FAM72B may serve as a novel biomarker in predicting the clinical prognosis and immune status for lung adenocarcinoma.
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Affiliation(s)
- Xinyan Li
- Department of Pharmacy, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xi Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yixiao Yuan
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - RuiQing Zhai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, Hong Kong SAR, China
- *Correspondence: Xiulin Jiang, ; William C. Cho,
| | - Xiulin Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Xiulin Jiang, ; William C. Cho,
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19
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Summers KM, Bush SJ, Wu C, Hume DA. Generation and network analysis of an RNA-seq transcriptional atlas for the rat. NAR Genom Bioinform 2022; 4:lqac017. [PMID: 35265836 PMCID: PMC8900154 DOI: 10.1093/nargab/lqac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/13/2022] [Accepted: 02/15/2022] [Indexed: 12/19/2022] Open
Abstract
Abstract
The laboratory rat is an important model for biomedical research. To generate a comprehensive rat transcriptomic atlas, we curated and downloaded 7700 rat RNA-seq datasets from public repositories, downsampled them to a common depth and quantified expression. Data from 585 rat tissues and cells, averaged from each BioProject, can be visualized and queried at http://biogps.org/ratatlas. Gene co-expression network (GCN) analysis revealed clusters of transcripts that were tissue or cell type restricted and contained transcription factors implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes. Many of these clusters overlap with previous data from analysis of other species, while some (e.g. expressed specifically in immune cells, retina/pineal gland, pituitary and germ cells) are unique to these data. GCN analysis on large subsets of the data related specifically to liver, nervous system, kidney, musculoskeletal system and cardiovascular system enabled deconvolution of cell type-specific signatures. The approach is extensible and the dataset can be used as a point of reference from which to analyse the transcriptomes of cell types and tissues that have not yet been sampled. Sets of strictly co-expressed transcripts provide a resource for critical interpretation of single-cell RNA-seq data.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Chunlei Wu
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David A Hume
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
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20
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Zinovyev A, Sadovsky M, Calzone L, Fouché A, Groeneveld CS, Chervov A, Barillot E, Gorban AN. Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches. Front Mol Biosci 2022; 8:793912. [PMID: 35178429 PMCID: PMC8846220 DOI: 10.3389/fmolb.2021.793912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Cell cycle is a biological process underlying the existence and propagation of life in time and space. It has been an object for mathematical modeling for long, with several alternative mechanistic modeling principles suggested, describing in more or less details the known molecular mechanisms. Recently, cell cycle has been investigated at single cell level in snapshots of unsynchronized cell populations, exploiting the new methods for transcriptomic and proteomic molecular profiling. This raises a need for simplified semi-phenomenological cell cycle models, in order to formalize the processes underlying the cell cycle, at a higher abstracted level. Here we suggest a modeling framework, recapitulating the most important properties of the cell cycle as a limit trajectory of a dynamical process characterized by several internal states with switches between them. In the simplest form, this leads to a limit cycle trajectory, composed by linear segments in logarithmic coordinates describing some extensive (depending on system size) cell properties. We prove a theorem connecting the effective embedding dimensionality of the cell cycle trajectory with the number of its linear segments. We also develop a simplified kinetic model with piecewise-constant kinetic rates describing the dynamics of lumps of genes involved in S-phase and G2/M phases. We show how the developed cell cycle models can be applied to analyze the available single cell datasets and simulate certain properties of the observed cell cycle trajectories. Based on our model, we can predict with good accuracy the cell line doubling time from the length of cell cycle trajectory.
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Affiliation(s)
- Andrei Zinovyev
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
- *Correspondence: Andrei Zinovyev,
| | - Michail Sadovsky
- Institute of Computational Modeling (RAS), Krasnoyarsk, Russia
- Laboratory of Medical Cybernetics, V.F.Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Federal Research and Clinic Center of FMBA of Russia, Krasnoyarsk, Russia
- Laboratory of Advanced Methods for High-Dimensional Data Analysis, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Laurence Calzone
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Aziz Fouché
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Clarice S. Groeneveld
- Cartes d’Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
- Oncologie Moleculaire, UMR144, Institut Curie, Paris, France
| | - Alexander Chervov
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Paris, France
- INSERM, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France
| | - Alexander N. Gorban
- Laboratory of Advanced Methods for High-Dimensional Data Analysis, Lobachevsky University, Nizhniy Novgorod, Russia
- Department of Mathematics, University of Leicester, Leicester, United Kingdom
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21
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Lehmann J, Narcisi R, Franceschini N, Chatzivasileiou D, Boer CG, Koevoet WJLM, Putavet D, Drabek D, van Haperen R, de Keizer PLJ, van Osch GJVM, Ten Berge D. WNT/beta-catenin signalling interrupts a senescence-induction cascade in human mesenchymal stem cells that restricts their expansion. Cell Mol Life Sci 2022; 79:82. [PMID: 35048158 PMCID: PMC8770385 DOI: 10.1007/s00018-021-04035-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 10/18/2021] [Accepted: 11/09/2021] [Indexed: 12/23/2022]
Abstract
Senescence, the irreversible cell cycle arrest of damaged cells, is accompanied by a deleterious pro-inflammatory senescence-associated secretory phenotype (SASP). Senescence and the SASP are major factors in aging, cancer, and degenerative diseases, and interfere with the expansion of adult cells in vitro, yet little is known about how to counteract their induction and deleterious effects. Paracrine signals are increasingly recognized as important senescence triggers and understanding their regulation and mode of action may provide novel opportunities to reduce senescence-induced inflammation and improve cell-based therapies. Here, we show that the signalling protein WNT3A counteracts the induction of paracrine senescence in cultured human adult mesenchymal stem cells (MSCs). We find that entry into senescence in a small subpopulation of MSCs triggers a secretome that causes a feed-forward signalling cascade that with increasing speed induces healthy cells into senescence. WNT signals interrupt this cascade by repressing cytokines that mediate this induction of senescence. Inhibition of those mediators by interference with NF-κB or interleukin 6 signalling reduced paracrine senescence in absence of WNT3A and promoted the expansion of MSCs. Our work reveals how WNT signals can antagonize senescence and has relevance not only for expansion of adult cells but can also provide new insights into senescence-associated inflammatory and degenerative diseases.
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Affiliation(s)
- Johannes Lehmann
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Center for Molecular Medicine, Section Molecular Cancer Research, Division LAB, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roberto Narcisi
- Department of Orthopaedics and Sports Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Natasja Franceschini
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Danai Chatzivasileiou
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cindy G Boer
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Wendy J L M Koevoet
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Diana Putavet
- Center for Molecular Medicine, Section Molecular Cancer Research, Division LAB, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Harbour Biomed, Rotterdam, the Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Harbour Biomed, Rotterdam, the Netherlands
| | - Peter L J de Keizer
- Center for Molecular Medicine, Section Molecular Cancer Research, Division LAB, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Gerjo J V M van Osch
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Department of Orthopaedics and Sports Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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22
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Abuaita BH, Lawrence ALE, Berger RP, Hill DR, Huang S, Yadagiri VK, Bons B, Fields C, Wobus CE, Spence JR, Young VB, O’Riordan MX. Comparative transcriptional profiling of the early host response to infection by typhoidal and non-typhoidal Salmonella serovars in human intestinal organoids. PLoS Pathog 2021; 17:e1009987. [PMID: 34669717 PMCID: PMC8570492 DOI: 10.1371/journal.ppat.1009987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/05/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
Salmonella enterica represents over 2500 serovars associated with a wide-ranging spectrum of disease; from self-limiting gastroenteritis to invasive infections caused by non-typhoidal serovars (NTS) and typhoidal serovars, respectively. Host factors strongly influence infection outcome as malnourished or immunocompromised individuals can develop invasive infections from NTS, however, comparative analyses of serovar-specific host responses have been constrained by reliance on limited model systems. Here we used human intestinal organoids (HIOs), a three-dimensional “gut-like” in vitro system derived from human embryonic stem cells, to elucidate similarities and differences in host responses to NTS and typhoidal serovars. HIOs discriminated between the two most prevalent NTS, Salmonella enterica serovar Typhimurium (STM) and Salmonella enterica serovar Enteritidis (SE), and typhoidal serovar Salmonella enterica serovar Typhi (ST) in epithelial cell invasion, replication and transcriptional responses. Pro-inflammatory signaling and cytokine output was reduced in ST-infected HIOs compared to NTS infections, consistent with early stages of NTS and typhoidal diseases. While we predicted that ST would induce a distinct transcriptional profile from the NTS strains, more nuanced expression profiles emerged. Notably, pathways involved in cell cycle, metabolism and mitochondrial functions were downregulated in STM-infected HIOs and upregulated in SE-infected HIOs. These results correlated with suppression of cellular proliferation and induction of host cell death in STM-infected HIOs and in contrast, elevated levels of reactive oxygen species production in SE-infected HIOs. Collectively, these results suggest that the HIO model is well suited to reveal host transcriptional programming specific to infection by individual Salmonella serovars, and that individual NTS may provoke unique host epithelial responses during intestinal stages of infection. Salmonella enterica is the major causative agent of bacterial infections associated with contaminated food and water. Salmonella enterica consists of over 2500 serovars of which Typhimurium (STM), Enteritidis (SE) and Typhi (ST) are the three major serovars with medical relevance to humans. These serovars elicit distinctive immune responses and cause different diseases in humans, including self-limiting diarrhea, gastroenteritis and typhoid fever. Differences in the human host response to these serovars are likely to be a major contributing factor to distinct disease outcomes but are not well characterized, possibly due to the limitations of human-derived physiological infection models. Distinct from immortalized epithelial cell culture models, human intestinal organoids (HIOs) are three-dimensional structures derived from embryonic stem cells that differentiate into intestinal mesenchymal and epithelial cells, mirroring key organizational aspects of the intestine. In this study, we used HIOs to monitor transcriptional changes during early stages of STM, SE and ST infection. Our comparative analysis showed that HIO inflammatory responses are the dominant response in all infections, but ST infection induces the weakest upregulation of inflammatory mediators relative to the other serovars. In addition, we identified several cellular processes, including cell cycle and mitochondrial functions, that were inversely regulated between STM and SE infection despite these serovars causing similar localized intestinal infection in humans. Our findings reinforce HIOs as an emerging model system to study Salmonella serovar infection and define global host transcriptional response profiles as a foundation for understanding human infection outcomes.
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Affiliation(s)
- Basel H. Abuaita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Anna-Lisa E. Lawrence
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan P. Berger
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - David R. Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sha Huang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Veda K. Yadagiri
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brooke Bons
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Courtney Fields
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jason R. Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Vincent B. Young
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mary X. O’Riordan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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23
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Wang F, Weng Z, Song H, Bao Y, Sui H, Fang Y, Tang X, Shen X. Ferric ammonium citrate (FAC)-induced inhibition of osteoblast proliferation/differentiation and its reversal by soybean-derived peptides (SDP). Food Chem Toxicol 2021; 156:112527. [PMID: 34464636 DOI: 10.1016/j.fct.2021.112527] [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: 09/06/2020] [Revised: 08/22/2021] [Accepted: 08/27/2021] [Indexed: 11/25/2022]
Abstract
Ferric citrate has been used to treat hyperphosphatemia, a prevalent symptom in patients with chronic kidney disease while ferric ammonium citrate (FAC), a more dissolvable format, is widely used as food additive. However, excess iron is associated with osteoporosis. Dietary soybean products have been shown to prevent the progression of osteoporosis. In this study, a group of peptides, referred as P3, was identified from the enzymolysis of soybean protein isolates, and its biological functions were investigated. The results showed that MC3T3-E1 cell cycle progression from G0/G1 to S phase was accelerated by P3 treatment. MC3T3-E1 cell proliferation was enhanced by P3 via ERK1/2 activation. Importantly, P3 treatment abolished the antiproliferative effect of FAC on MC3T3-E1 cell. In addition, P3 treatment increased the expression of ALP, COL-1, OCN, consequently promoting the differentiation and mineralization of MC3T3-E1 cells via activation of p38 MAPK pathway. Consequently, P3 treatment was able to reverse the inhibitory effect of FAC on osteoblasts differentiation and mineralization. Our findings suggest P3, as a dietary supplement, has a potential therapeutic function to attenuate the adverse effects of FAC on bone metabolism and to prevent osteoporosis progression.
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Affiliation(s)
- Fang Wang
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, 210023, China
| | - Zebin Weng
- School of Traditional Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Haizhao Song
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, 210023, China
| | - Yifang Bao
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, 210023, China
| | - Huilin Sui
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, 210023, China
| | - Yong Fang
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, 210023, China
| | - Xiaozhi Tang
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, 210023, China
| | - Xinchun Shen
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, 210023, China.
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24
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Herrera-Uribe J, Wiarda JE, Sivasankaran SK, Daharsh L, Liu H, Byrne KA, Smith TPL, Lunney JK, Loving CL, Tuggle CK. Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing. Front Genet 2021; 12:689406. [PMID: 34249103 PMCID: PMC8261551 DOI: 10.3389/fgene.2021.689406] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023] Open
Abstract
Pigs are a valuable human biomedical model and an important protein source supporting global food security. The transcriptomes of peripheral blood immune cells in pigs were defined at the bulk cell-type and single cell levels. First, eight cell types were isolated in bulk from peripheral blood mononuclear cells (PBMCs) by cell sorting, representing Myeloid, NK cells and specific populations of T and B-cells. Transcriptomes for each bulk population of cells were generated by RNA-seq with 10,974 expressed genes detected. Pairwise comparisons between cell types revealed specific expression, while enrichment analysis identified 1,885 to 3,591 significantly enriched genes across all 8 cell types. Gene Ontology analysis for the top 25% of significantly enriched genes (SEG) showed high enrichment of biological processes related to the nature of each cell type. Comparison of gene expression indicated highly significant correlations between pig cells and corresponding human PBMC bulk RNA-seq data available in Haemopedia. Second, higher resolution of distinct cell populations was obtained by single-cell RNA-sequencing (scRNA-seq) of PBMC. Seven PBMC samples were partitioned and sequenced that produced 28,810 single cell transcriptomes distributed across 36 clusters and classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, B-cell, conventional CD4 and CD8 αβ T-cells, NK cells, and γδ T-cells. Signature gene sets from the human Haemopedia data were assessed for relative enrichment in genes expressed in pig cells and integration of pig scRNA-seq with a public human scRNA-seq dataset provided further validation for similarity between human and pig data. The sorted porcine bulk RNAseq dataset informed classification of scRNA-seq PBMC populations; specifically, an integration of the datasets showed that the pig bulk RNAseq data helped define the CD4CD8 double-positive T-cell populations in the scRNA-seq data. Overall, the data provides deep and well-validated transcriptomic data from sorted PBMC populations and the first single-cell transcriptomic data for porcine PBMCs. This resource will be invaluable for annotation of pig genes controlling immunogenetic traits as part of the porcine Functional Annotation of Animal Genomes (FAANG) project, as well as further study of, and development of new reagents for, porcine immunology.
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Jayne E. Wiarda
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
- Immunobiology Graduate Program, Iowa State University, Ames, IA, United States
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, United States
| | - Sathesh K. Sivasankaran
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
- Genome Informatics Facility, Iowa State University, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kristen A. Byrne
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | | | - Joan K. Lunney
- USDA-ARS, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States
| | - Crystal L. Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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25
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Gažová I, Lefevre L, Bush SJ, Rojo R, Hume DA, Lengeling A, Summers KM. CRISPR-Cas9 Editing of Human Histone Deubiquitinase Gene USP16 in Human Monocytic Leukemia Cell Line THP-1. Front Cell Dev Biol 2021; 9:679544. [PMID: 34136489 PMCID: PMC8203323 DOI: 10.3389/fcell.2021.679544] [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: 03/12/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022] Open
Abstract
USP16 is a histone deubiquitinase which facilitates G2/M transition during the cell cycle, regulates DNA damage repair and contributes to inducible gene expression. We mutated the USP16 gene in a high differentiation clone of the acute monocytic leukemia cell line THP-1 using the CRISPR-Cas9 system and generated four homozygous knockout clones. All were able to proliferate and to differentiate in response to phorbol ester (PMA) treatment. One line was highly proliferative prior to PMA treatment and shut down proliferation upon differentiation, like wild type. Three clones showed sustained expression of the progenitor cell marker MYB, indicating that differentiation had not completely blocked proliferation in these clones. Network analysis of transcriptomic differences among wild type, heterozygotes and homozygotes showed clusters of genes that were up- or down-regulated after differentiation in all cell lines. Prior to PMA treatment, the homozygous clones had lower levels than wild type of genes relating to metabolism and mitochondria, including SRPRB, encoding an interaction partner of USP16. There was also apparent loss of interferon signaling. In contrast, a number of genes were up-regulated in the homozygous cells compared to wild type at baseline, including other deubiquitinases (USP12, BAP1, and MYSM1). However, three homozygotes failed to fully induce USP3 during differentiation. Other network clusters showed effects prior to or after differentiation in the homozygous clones. Thus the removal of USP16 affected the transcriptome of the cells, although all these lines were able to survive, which suggests that the functions attributed to USP16 may be redundant. Our analysis indicates that the leukemic line can adapt to the extreme selection pressure applied by the loss of USP16, and the harsh conditions of the gene editing and selection protocol, through different compensatory pathways. Similar selection pressures occur during the evolution of a cancer in vivo, and our results can be seen as a case study in leukemic cell adaptation. USP16 has been considered a target for cancer chemotherapy, but our results suggest that treatment would select for escape mutants that are resistant to USP16 inhibitors.
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Affiliation(s)
- Iveta Gažová
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Stephen J Bush
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Rocio Rojo
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - David A Hume
- Mater Research Institute - University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Andreas Lengeling
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - Kim M Summers
- The Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom.,Mater Research Institute - University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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26
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Miyashita S, Owa T, Seto Y, Yamashita M, Aida S, Sone M, Ichijo K, Nishioka T, Kaibuchi K, Kawaguchi Y, Taya S, Hoshino M. Cyclin D1 controls development of cerebellar granule cell progenitors through phosphorylation and stabilization of ATOH1. EMBO J 2021; 40:e105712. [PMID: 34057742 PMCID: PMC8280807 DOI: 10.15252/embj.2020105712] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 03/28/2021] [Accepted: 04/01/2021] [Indexed: 12/27/2022] Open
Abstract
During development, neural progenitors are in proliferative and immature states; however, the molecular machinery that cooperatively controls both states remains elusive. Here, we report that cyclin D1 (CCND1) directly regulates both proliferative and immature states of cerebellar granule cell progenitors (GCPs). CCND1 not only accelerates cell cycle but also upregulates ATOH1 protein, an essential transcription factor that maintains GCPs in an immature state. In cooperation with CDK4, CCND1 directly phosphorylates S309 of ATOH1, which inhibits additional phosphorylation at S328 and consequently prevents S328 phosphorylation-dependent ATOH1 degradation. Additionally, PROX1 downregulates Ccnd1 expression by histone deacetylation of Ccnd1 promoter in GCPs, leading to cell cycle exit and differentiation. Moreover, WNT signaling upregulates PROX1 expression in GCPs. These findings suggest that WNT-PROX1-CCND1-ATOH1 signaling cascade cooperatively controls proliferative and immature states of GCPs. We revealed that the expression and phosphorylation levels of these molecules dynamically change during cerebellar development, which are suggested to determine appropriate differentiation rates from GCPs to GCs at distinct developmental stages. This study contributes to understanding the regulatory mechanism of GCPs as well as neural progenitors.
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Affiliation(s)
- Satoshi Miyashita
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Tomoo Owa
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Yusuke Seto
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan.,Laboratory of Developmental Systems, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mariko Yamashita
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Shogo Aida
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan.,Department of Biomolecular Science, Faculty of Science, Toho University, Chiba, Japan
| | - Masaki Sone
- Department of Biomolecular Science, Faculty of Science, Toho University, Chiba, Japan
| | - Kentaro Ichijo
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan.,Department of Otolaryngology and Head and Neck Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoki Nishioka
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiya Kawaguchi
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shinichiro Taya
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
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Cleary CM, Milla BM, Kuo FS, James S, Flynn WF, Robson P, Mulkey DK. Somatostatin-expressing parafacial neurons are CO 2/H + sensitive and regulate baseline breathing. eLife 2021; 10:e60317. [PMID: 34013884 PMCID: PMC8169115 DOI: 10.7554/elife.60317] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 05/19/2021] [Indexed: 01/16/2023] Open
Abstract
Glutamatergic neurons in the retrotrapezoid nucleus (RTN) function as respiratory chemoreceptors by regulating breathing in response to tissue CO2/H+. The RTN and greater parafacial region may also function as a chemosensing network composed of CO2/H+-sensitive excitatory and inhibitory synaptic interactions. In the context of disease, we showed that loss of inhibitory neural activity in a mouse model of Dravet syndrome disinhibited RTN chemoreceptors and destabilized breathing (Kuo et al., 2019). Despite this, contributions of parafacial inhibitory neurons to control of breathing are unknown, and synaptic properties of RTN neurons have not been characterized. Here, we show the parafacial region contains a limited diversity of inhibitory neurons including somatostatin (Sst)-, parvalbumin (Pvalb)-, and cholecystokinin (Cck)-expressing neurons. Of these, Sst-expressing interneurons appear uniquely inhibited by CO2/H+. We also show RTN chemoreceptors receive inhibitory input that is withdrawn in a CO2/H+-dependent manner, and chemogenetic suppression of Sst+ parafacial neurons, but not Pvalb+ or Cck+ neurons, increases baseline breathing. These results suggest Sst-expressing parafacial neurons contribute to RTN chemoreception and respiratory activity.
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Affiliation(s)
- Colin M Cleary
- Department of Physiology and Neurobiology, University of ConnecticutStorrsUnited States
| | - Brenda M Milla
- Department of Physiology and Neurobiology, University of ConnecticutStorrsUnited States
| | - Fu-Shan Kuo
- Department of Physiology and Neurobiology, University of ConnecticutStorrsUnited States
| | - Shaun James
- Department of Physiology and Neurobiology, University of ConnecticutStorrsUnited States
| | - William F Flynn
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
| | - Paul Robson
- The Jackson Laboratory for Genomic MedicineFarmingtonUnited States
- Institute for Systems Genomics, University of ConnecticutFarmingtonUnited States
| | - Daniel K Mulkey
- Department of Physiology and Neurobiology, University of ConnecticutStorrsUnited States
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Sutcliffe DJ, Dinasarapu AR, Visser JE, Hoed JD, Seifar F, Joshi P, Ceballos-Picot I, Sardar T, Hess EJ, Sun YV, Wen Z, Zwick ME, Jinnah HA. Induced pluripotent stem cells from subjects with Lesch-Nyhan disease. Sci Rep 2021; 11:8523. [PMID: 33875724 PMCID: PMC8055678 DOI: 10.1038/s41598-021-87955-9] [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: 07/31/2020] [Accepted: 03/24/2021] [Indexed: 12/18/2022] Open
Abstract
Lesch-Nyhan disease (LND) is an inherited disorder caused by pathogenic variants in the HPRT1 gene, which encodes the purine recycling enzyme hypoxanthine-guanine phosphoribosyltransferase (HGprt). We generated 6 induced pluripotent stem cell (iPSC) lines from 3 individuals with LND, along with 6 control lines from 3 normal individuals. All 12 lines had the characteristics of pluripotent stem cells, as assessed by immunostaining for pluripotency markers, expression of pluripotency genes, and differentiation into the 3 primary germ cell layers. Gene expression profiling with RNAseq demonstrated significant heterogeneity among the lines. Despite this heterogeneity, several anticipated abnormalities were readily detectable across all LND lines, including reduced HPRT1 mRNA. Several unexpected abnormalities were also consistently detectable across the LND lines, including decreases in FAR2P1 and increases in RNF39. Shotgun proteomics also demonstrated several expected abnormalities in the LND lines, such as absence of HGprt protein. The proteomics study also revealed several unexpected abnormalities across the LND lines, including increases in GNAO1 decreases in NSE4A. There was a good but partial correlation between abnormalities revealed by the RNAseq and proteomics methods. Finally, functional studies demonstrated LND lines had no HGprt enzyme activity and resistance to the toxic pro-drug 6-thioguanine. Intracellular purines in the LND lines were normal, but they did not recycle hypoxanthine. These cells provide a novel resource to reveal insights into the relevance of heterogeneity among iPSC lines and applications for modeling LND.
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Affiliation(s)
- Diane J Sutcliffe
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Ashok R Dinasarapu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jasper E Visser
- Department of Neurology, Cognition and Behavior, Donders Institute for Brain, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neurology, Amphia Hospital, Breda, The Netherlands
| | - Joery den Hoed
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Fatemeh Seifar
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
- Neurosciences Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, 30322, USA
| | - Piyush Joshi
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Irene Ceballos-Picot
- Laboratoire de Biochimie Métabolomique Et Protéomique, Hôpital Universitaire Necker, Paris, France
| | - Tejas Sardar
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
| | - Ellen J Hess
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
- Neurosciences Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, 30322, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA. 30322, USA
| | - Zhexing Wen
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA
- Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - H A Jinnah
- Department of Neurology, Emory University School of Medicine, 101 Woodruff Circle, 6305 Woodruff Memorial Building, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Neurosciences Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, 30322, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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Ho NTT, Rahane CS, Pramanik S, Kim PS, Kutzner A, Heese K. FAM72, Glioblastoma Multiforme (GBM) and Beyond. Cancers (Basel) 2021; 13:cancers13051025. [PMID: 33804473 PMCID: PMC7957592 DOI: 10.3390/cancers13051025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Glioblastoma multiforme (GBM) is a serious and aggressive cancer disease that has not allowed scientists to rest for decades. In this review, we consider the new gene pair |-SRGAP2–FAM72-| and discuss its role in the cell cycle and the possibility of defining new therapeutic approaches for the treatment of GBM and other cancers via this gene pair |-SRGAP2–FAM72-|. Abstract Neural stem cells (NSCs) offer great potential for regenerative medicine due to their excellent ability to differentiate into various specialized cell types of the brain. In the central nervous system (CNS), NSC renewal and differentiation are under strict control by the regulation of the pivotal SLIT-ROBO Rho GTPase activating protein 2 (SRGAP2)—Family with sequence similarity 72 (FAM72) master gene (i.e., |-SRGAP2–FAM72-|) via a divergent gene transcription activation mechanism. If the gene transcription control unit (i.e., the intergenic region of the two sub-gene units, SRGAP2 and FAM72) gets out of control, NSCs may transform into cancer stem cells and generate brain tumor cells responsible for brain cancer such as glioblastoma multiforme (GBM). Here, we discuss the surveillance of this |-SRGAP2–FAM72-| master gene and its role in GBM, and also in light of FAM72 for diagnosing various types of cancers outside of the CNS.
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Affiliation(s)
- Nguyen Thi Thanh Ho
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
| | - Chinmay Satish Rahane
- Maharashtra Institute of Medical Education and Research, Talegaon Dabhade, Maharashtra 410507, India;
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany;
| | - Pok-Son Kim
- Department of Mathematics, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 136-702, Korea;
| | - Arne Kutzner
- Department of Information Systems, College of Computer Science, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea;
- Correspondence:
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30
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Pridans C, Irvine KM, Davis GM, Lefevre L, Bush SJ, Hume DA. Transcriptomic Analysis of Rat Macrophages. Front Immunol 2021; 11:594594. [PMID: 33633725 PMCID: PMC7902030 DOI: 10.3389/fimmu.2020.594594] [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: 08/13/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
The laboratory rat is widely used as a model for human diseases. Many of these diseases involve monocytes and tissue macrophages in different states of activation. Whilst methods for in vitro differentiation of mouse macrophages from embryonic stem cells (ESC) and bone marrow (BM) are well established, these are lacking for the rat. The gene expression profiles of rat macrophages have also not been characterised to the same extent as mouse. We have established the methodology for production of rat ESC-derived macrophages and compared their gene expression profiles to macrophages obtained from the lung and peritoneal cavity and those differentiated from BM and blood monocytes. We determined the gene signature of Kupffer cells in the liver using rats deficient in macrophage colony stimulating factor receptor (CSF1R). We also examined the response of BM-derived macrophages to lipopolysaccharide (LPS). The results indicate that many, but not all, tissue-specific adaptations observed in mice are conserved in the rat. Importantly, we show that unlike mice, rat macrophages express the CSF1R ligand, colony stimulating factor 1 (CSF1).
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Affiliation(s)
- Clare Pridans
- Centre for Inflammation Research, University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Katharine M. Irvine
- Mater Research Institute Mater Research Institute – University of Queensland, Brisbane, QLD, Australia
| | - Gemma M. Davis
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Lucas Lefevre
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Headington, United Kingdom
| | - David A. Hume
- Mater Research Institute Mater Research Institute – University of Queensland, Brisbane, QLD, Australia
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31
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HEDGEHOG/GLI Modulates the PRR11-SKA2 Bidirectional Transcription Unit in Lung Squamous Cell Carcinomas. Genes (Basel) 2021; 12:genes12010120. [PMID: 33477943 PMCID: PMC7833434 DOI: 10.3390/genes12010120] [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: 11/11/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
We previously demonstrated that proline-rich protein 11 (PRR11) and spindle and kinetochore associated 2 (SKA2) constituted a head-to-head gene pair driven by a prototypical bidirectional promoter. This gene pair synergistically promoted the development of non-small cell lung cancer. However, the signaling pathways leading to the ectopic expression of this gene pair remains obscure. In the present study, we first analyzed the lung squamous cell carcinoma (LSCC) relevant RNA sequencing data from The Cancer Genome Atlas (TCGA) database using the correlation analysis of gene expression and gene set enrichment analysis (GSEA), which revealed that the PRR11-SKA2 correlated gene list highly resembled the Hedgehog (Hh) pathway activation-related gene set. Subsequently, GLI1/2 inhibitor GANT-61 or GLI1/2-siRNA inhibited the Hh pathway of LSCC cells, concomitantly decreasing the expression levels of PRR11 and SKA2. Furthermore, the mRNA expression profile of LSCC cells treated with GANT-61 was detected using RNA sequencing, displaying 397 differentially expressed genes (203 upregulated genes and 194 downregulated genes). Out of them, one gene set, including BIRC5, NCAPG, CCNB2, and BUB1, was involved in cell division and interacted with both PRR11 and SKA2. These genes were verified as the downregulated genes via RT-PCR and their high expression significantly correlated with the shorter overall survival of LSCC patients. Taken together, our results indicate that GLI1/2 mediates the expression of the PRR11-SKA2-centric gene set that serves as an unfavorable prognostic indicator for LSCC patients, potentializing new combinatorial diagnostic and therapeutic strategies in LSCC.
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Machaliński B, Rogińska D, Wilk A, Szumilas K, Prowans P, Paczkowska E, Szumilas P, Stecewicz I, Zawodny P, Ziętek M, Wiszniewska B. Global Gene Expression of Cultured Human Dermal Fibroblasts: Focus on Cell Cycle and Proliferation Status in Improving the Condition of Face Skin. Int J Med Sci 2021; 18:1519-1531. [PMID: 33628110 PMCID: PMC7893558 DOI: 10.7150/ijms.46265] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Chronological skin ageing is an inevitable physiological process that results in thin and sagging skin, fine wrinkles, and gradual dermal atrophy. The main therapeutic approaches to soft tissue augmentation involve using dermal fillers, where natural fillers, such as autologous fibroblasts, are involved in generating dermal matrix proteins. The aim of this study was to determine the global transcriptome profile of three passages of dermal autologous fibroblasts from a male volunteer, focusing on the processes of the cell cycle and cell proliferation status to estimate the optimal passage of the tested cells with respect to their reimplantation. We performed K-means clustering and validation of the expression of the selected mRNA by qRT-PCR. Ten genes were selected (ANLN, BUB1, CDC20, CCNA2, DLGAP5, MKI67, PLK1, PRC1, SPAG5, and TPX2) from the top five processes annotated to cluster 5. Detailed microarray analysis of the fibroblast genes indicated that the cell population of the third passage exhibited the highest number of upregulated genes involved in the cell cycle and cell proliferation. In all cases, the results of qRT-PCR confirmed the differences in expression of the selected mRNAs between fibroblasts from the primary culture (C0) and from the first (C1), second (C2), and third (C3) cell passage. Our results thus suggest that these cells might be useful for increasing fibroblast numbers after reimplantation into a recipient's skin, and the method used in this study seems to be an excellent tool for autologous transplantation allowing the rejuvenation of aging skin.
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Affiliation(s)
- Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Dorota Rogińska
- Department of General Pathology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Aleksandra Wilk
- Department of Histology and Embryology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Kamila Szumilas
- Department of Physiology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Piotr Prowans
- Department of General Pathology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Edyta Paczkowska
- Department of General Pathology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Paweł Szumilas
- Department of Social Medicine and Public Health, Chair of Social Medicine, Pomeranian Medical University, Żołnierska 48, 71-210 Szczecin, Poland
| | - Iwona Stecewicz
- Department of General Pathology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Piotr Zawodny
- Department of General Pathology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Maciej Ziętek
- Department of General Pathology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
| | - Barbara Wiszniewska
- Department of Histology and Embryology, Pomeranian Medical University, Powstanców Wlkp. 72, 70-111 Szczecin, Poland
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Yu H, Li Y, Li L, Huang J, Wang X, Tang R, Jiang Z, Lv L, Chen F, Yu C, Yuan K. Functional reciprocity of proteins involved in mitosis and endocytosis. FEBS J 2020; 288:5850-5866. [PMID: 33300206 DOI: 10.1111/febs.15664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/29/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
Mitosis and endocytosis are two fundamental cellular processes essential for maintaining a eukaryotic life. Mitosis partitions duplicated chromatin enveloped in the nuclear membrane into two new cells, whereas endocytosis takes in extracellular substances through membrane invagination. These two processes are spatiotemporally separated and seemingly unrelated. However, recent studies have uncovered that endocytic proteins have moonlighting functions in mitosis, and mitotic complexes manifest additional roles in endocytosis. In this review, we summarize important proteins or protein complexes that participate in both processes, compare their mechanism of action, and discuss the rationale behind this multifunctionality. We also speculate on the possible origin of the functional reciprocity from an evolutionary perspective.
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Affiliation(s)
- Haibin Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yinshuang Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Li Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | | | - Xujuan Wang
- The High School Attached to Hunan Normal University, Changsha, China
| | - Ruijun Tang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Zhenghui Jiang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,The Biobank of Xiangya Hospital, Central South University, Changsha, China
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34
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Summers KM, Bush SJ, Hume DA. Network analysis of transcriptomic diversity amongst resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system. PLoS Biol 2020; 18:e3000859. [PMID: 33031383 PMCID: PMC7575120 DOI: 10.1371/journal.pbio.3000859] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/20/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The mononuclear phagocyte system (MPS) is a family of cells including progenitors, circulating blood monocytes, resident tissue macrophages, and dendritic cells (DCs) present in every tissue in the body. To test the relationships between markers and transcriptomic diversity in the MPS, we collected from National Center for Biotechnology Information Gene Expression Omnibus (NCBI-GEO) a total of 466 quality RNA sequencing (RNA-seq) data sets generated from mouse MPS cells isolated from bone marrow, blood, and multiple tissues. The primary data were randomly downsized to a depth of 10 million reads and requantified. The resulting data set was clustered using the network analysis tool BioLayout. A sample-to-sample matrix revealed that MPS populations could be separated based upon tissue of origin. Cells identified as classical DC subsets, cDC1s and cDC2s, and lacking Fcgr1 (encoding the protein CD64) were contained within the MPS cluster, no more distinct than other MPS cells. A gene-to-gene correlation matrix identified large generic coexpression clusters associated with MPS maturation and innate immune function. Smaller coexpression gene clusters, including the transcription factors that drive them, showed higher expression within defined isolated cells, including monocytes, macrophages, and DCs isolated from specific tissues. They include a cluster containing Lyve1 that implies a function in endothelial cell (EC) homeostasis, a cluster of transcripts enriched in intestinal macrophages, and a generic lymphoid tissue cDC cluster associated with Ccr7. However, transcripts encoding Adgre1, Itgax, Itgam, Clec9a, Cd163, Mertk, Mrc1, Retnla, and H2-a/e (encoding class II major histocompatibility complex [MHC] proteins) and many other proposed macrophage subset and DC lineage markers each had idiosyncratic expression profiles. Coexpression of immediate early genes (for example, Egr1, Fos, Dusp1) and inflammatory cytokines and chemokines (tumour necrosis factor [Tnf], Il1b, Ccl3/4) indicated that all tissue disaggregation and separation protocols activate MPS cells. Tissue-specific expression clusters indicated that all cell isolation procedures also co-purify other unrelated cell types that may interact with MPS cells in vivo. Comparative analysis of RNA-seq and single-cell RNA-seq (scRNA-seq) data from the same lung cell populations indicated that MPS heterogeneity implied by global cluster analysis may be even greater at a single-cell level. This analysis highlights the power of large data sets to identify the diversity of MPS cellular phenotypes and the limited predictive value of surface markers to define lineages, functions, or subpopulations.
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Affiliation(s)
- Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
- * E-mail:
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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dusinska M, Musak L, Vodicka P, Hemminki K, Försti A. Impact of genetic polymorphisms in kinetochore and spindle assembly genes on chromosomal aberration frequency in healthy humans. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 858-860:503253. [PMID: 33198934 DOI: 10.1016/j.mrgentox.2020.503253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/24/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
Genomic instability is a characteristic of a majority of human malignancies. Chromosomal instability is a common form of genomic instability that can be caused by defects in mitotic checkpoint genes. Chromosomal aberrations in peripheral blood are also indicative of genotoxic exposure and potential cancer risk. We evaluated associations between inherited genetic variants in 33 mitotic checkpoint genes and the frequency of chromosomal aberrations (CAs) in the presence and absence of environmental genotoxic exposure. Associations with both chromosome and chromatid type of aberrations were evaluated in two cohorts of healthy individuals, namely an exposed and a reference group consisting of 607 and 866 individuals, respectively. Binary logistic and linear regression analyses were performed for the association studies. Bonferroni-corrected significant p-value was 5 × 10-4 for 99 tests based on the number of analyzed genes and phenotypes. In the reference group the most prominent associations were found with variants in CCNB1, a master regulator of mitosis, and in genes involved in kinetochore function, including CENPH and TEX14, whereas in the exposed group the main association was found with variants in TTK, also an important gene in kinetochore function. How the identified variants may affect the fidelity of mitotic checkpoint remains to be investigated, however, the present study suggests that genetic variation may partly explain interindividual variation in the formation of CAs.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany; GeneWerk GmbH, Im Neuenheimer Feld 582, 6910, Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505, Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605, Pilsen, Czech Republic
| | - Soňa Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605, Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03, Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn School of Medicine and University of Bonn, D-53127, Bonn, Germany; Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine and University of Bonn, D-53127, Bonn, Germany
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2007, Kjeller, Norway
| | - Ludovit Musak
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Malá Hora(4D), 03601, Martin, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605, Pilsen, Czech Republic
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605, Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
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36
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Markby GR, Macrae VE, Corcoran BM, Summers KM. Comparative transcriptomic profiling of myxomatous mitral valve disease in the cavalier King Charles spaniel. BMC Vet Res 2020; 16:350. [PMID: 32967675 PMCID: PMC7509937 DOI: 10.1186/s12917-020-02542-w] [Citation(s) in RCA: 4] [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: 04/17/2020] [Accepted: 08/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Almost all elderly dogs develop myxomatous mitral valve disease by the end of their life, but the cavalier King Charles spaniel (CKCS) has a heightened susceptibility, frequently resulting in death at a young age and suggesting that there is a genetic component to the condition in this breed. Transcriptional profiling can reveal the impact of genetic variation through differences in gene expression levels. The aim of this study was to determine whether expression patterns were different in mitral valves showing myxomatous degeneration from CKCS dogs compared to valves from non-CKCS dogs. RESULTS Gene expression patterns in three groups of canine valves resulted in distinct separation of normal valves, diseased valves from CKCS and diseased valves from other breeds; the latter were more similar to the normal valves than were the valves from CKCS. Gene expression patterns in diseased valves from CKCS dogs were quite different from those in the valves from other dogs, both affected and normal. Patterns in all diseased valves (from CKCS and other breeds) were also somewhat different from normal non-diseased samples. Analysis of differentially expressed genes showed enrichment in GO terms relating to cardiac development and function and to calcium signalling canonical pathway in the genes down-regulated in the diseased valves from CKCS, compared to normal valves and to diseased valves from other breeds. F2 (prothrombin) (CKCS diseased valves compared to normal) and MEF2C pathway activation (CKCS diseased valves compared to non-CKCS diseased valves) had the strongest association with the gene changes. A large number of genes that were differentially expressed in the CKCS diseased valves compared with normal valves and diseased valves from other breeds were associated with cardiomyocytes including CASQ2, TNNI3 and RYR2. CONCLUSION Transcriptomic profiling identified gene expression changes in CKCS diseased valves that were not present in age and disease severity-matched non-CKCS valves. These genes are associated with cardiomyocytes, coagulation and extra-cellular matrix remodelling. Identification of genes that vary in the CKCS will allow exploration of genetic variation to understand the aetiology of the disease in this breed, and ultimately development of breeding strategies to eliminate this disease from the breed.
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Affiliation(s)
- G R Markby
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG
| | - V E Macrae
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG
| | - B M Corcoran
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG.
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG.
| | - K M Summers
- The Roslin Institute, University of Edinburgh, Roslin Mid-Lothian, Roslin, Scotland, UK, EH25 9RG
- Mater Research Institute-University of Queensland, 37 Kent St, Woolloongabba, QLD, 4102, Australia
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37
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Lafranchi L, Müllers E, Rutishauser D, Lindqvist A. FRET-Based Sorting of Live Cells Reveals Shifted Balance between PLK1 and CDK1 Activities During Checkpoint Recovery. Cells 2020; 9:E2126. [PMID: 32961751 PMCID: PMC7564076 DOI: 10.3390/cells9092126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022] Open
Abstract
Cells recovering from the G2/M DNA damage checkpoint rely more on Aurora A-PLK1 signaling than cells progressing through an unperturbed G2 phase, but the reason for this discrepancy is not known. Here, we devised a method based on a FRET reporter for PLK1 activity to sort cells in distinct populations within G2 phase. We employed mass spectroscopy to characterize changes in protein levels through an unperturbed G2 phase and validated that ATAD2 levels decrease in a proteasome-dependent manner. Comparing unperturbed cells with cells recovering from DNA damage, we note that at similar PLK1 activities, recovering cells contain higher levels of Cyclin B1 and increased phosphorylation of CDK1 targets. The increased Cyclin B1 levels are due to continuous Cyclin B1 production during a DNA damage response and are sustained until mitosis. Whereas partial inhibition of PLK1 suppresses mitotic entry more efficiently when cells recover from a checkpoint, partial inhibition of CDK1 suppresses mitotic entry more efficiently in unperturbed cells. Our findings provide a resource for proteome changes during G2 phase, show that the mitotic entry network is rewired during a DNA damage response, and suggest that the bottleneck for mitotic entry shifts from CDK1 to PLK1 after DNA damage.
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Affiliation(s)
- Lorenzo Lafranchi
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (L.L.); (E.M.)
| | - Erik Müllers
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (L.L.); (E.M.)
| | - Dorothea Rutishauser
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;
- Science for Life Laboratory, SE-171 65 Stockholm, Sweden
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (L.L.); (E.M.)
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38
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Wang C, Chen Z, Su D, Tang M, Nie L, Zhang H, Feng X, Wang R, Shen X, Srivastava M, McLaughlin ME, Hart T, Li L, Chen J. C17orf53 is identified as a novel gene involved in inter-strand crosslink repair. DNA Repair (Amst) 2020; 95:102946. [PMID: 32853826 DOI: 10.1016/j.dnarep.2020.102946] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/22/2020] [Accepted: 07/31/2020] [Indexed: 01/05/2023]
Abstract
Ataxia Telangiectasia and Rad3-Related kinase (ATR) is a master regulator of genome maintenance, and participates in DNA replication and various DNA repair pathways. In a genome-wide screen for ATR-dependent fitness genes, we identified a previously uncharacterized gene, C17orf53, whose loss led to hypersensitivity to ATR inhibition. C17orf53 is conserved in vertebrates and is required for efficient cell proliferation. Loss of C17orf53 slowed down DNA replication and led to pronounced interstrand crosslink (ICL) repair defect. We showed that C17orf53 is a ssDNA- and RPA-binding protein and both characteristics are important for its functions in the cell. In addition, using multiple omics methods, we found that C17orf53 works with MCM8/9 to promote cell survival in response to ICL lesions. Taken together, our data suggest that C17orf53 is a novel component involved in ICL repair pathway.
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Affiliation(s)
- Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rui Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Megan E McLaughlin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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39
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Bush SJ, McCulloch MEB, Lisowski ZM, Muriuki C, Clark EL, Young R, Pridans C, Prendergast JGD, Summers KM, Hume DA. Species-Specificity of Transcriptional Regulation and the Response to Lipopolysaccharide in Mammalian Macrophages. Front Cell Dev Biol 2020; 8:661. [PMID: 32793601 PMCID: PMC7386301 DOI: 10.3389/fcell.2020.00661] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 02/02/2023] Open
Abstract
Mammalian macrophages differ in their basal gene expression profiles and response to the toll-like receptor 4 (TLR4) agonist, lipopolysaccharide (LPS). In human macrophages, LPS elicits a temporal cascade of transient gene expression including feed forward activators and feedback regulators that limit the response. Here we present a transcriptional network analysis of the response of sheep bone marrow-derived macrophages (BMDM) to LPS based upon RNA-seq at 0, 2, 4, 7, and 24 h post-stimulation. The analysis reveals a conserved transcription factor network with humans, and rapid induction of feedback regulators that constrain the response at every level. The gene expression profiles of sheep BMDM at 0 and 7 h post LPS addition were compared to similar data obtained from goat, cow, water buffalo, horse, pig, mouse and rat BMDM. This comparison was based upon identification of 8,200 genes annotated in all species and detected at >10TPM in at least one sample. Analysis of expression of transcription factors revealed a conserved transcriptional millieu associated with macrophage differentiation and LPS response. The largest co-expression clusters, including genes encoding cell surface receptors, endosome–lysosome components and secretory activity, were also expressed in all species and the combined dataset defines a macrophage functional transcriptome. All of the large animals differed from rodents in lacking inducible expression of genes involved in arginine metabolism and nitric oxide production. Instead, they expressed inducible transporters and enzymes of tryptophan and kynurenine metabolism. BMDM from all species expressed high levels of transcripts encoding transporters and enzymes involved in glutamine metabolism suggesting that glutamine is a major metabolic fuel. We identify and discuss transcripts that were uniquely expressed or regulated in rodents compared to large animals including ACOD1, CXC and CC chemokines, CD163, CLEC4E, CPM, CSF1, CSF2, CTSK, MARCO, MMP9, SLC2A3, SLC7A7, and SUCNR1. Conversely, the data confirm the conserved regulation of multiple transcripts for which there is limited functional data from mouse models and knockouts. The data provide a resource for functional annotation and interpretation of loci involved in susceptibility to infectious and inflammatory disease in humans and large animal species.
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Affiliation(s)
- Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mary E B McCulloch
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Zofia M Lisowski
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Charity Muriuki
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Emily L Clark
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Rachel Young
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Clare Pridans
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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40
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Gažová I, Lefevre L, Bush SJ, Clohisey S, Arner E, de Hoon M, Severin J, van Duin L, Andersson R, Lengeling A, Hume DA, Summers KM. The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1. Front Cell Dev Biol 2020; 8:498. [PMID: 32719792 PMCID: PMC7347797 DOI: 10.3389/fcell.2020.00498] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
The response of the human acute myeloid leukemia cell line THP-1 to phorbol esters has been widely studied to test candidate leukemia therapies and as a model of cell cycle arrest and monocyte-macrophage differentiation. Here we have employed Cap Analysis of Gene Expression (CAGE) to analyze a dense time course of transcriptional regulation in THP-1 cells treated with phorbol myristate acetate (PMA) over 96 h. PMA treatment greatly reduced the numbers of cells entering S phase and also blocked cells exiting G2/M. The PMA-treated cells became adherent and expression of mature macrophage-specific genes increased progressively over the duration of the time course. Within 1–2 h PMA induced known targets of tumor protein p53 (TP53), notably CDKN1A, followed by gradual down-regulation of cell-cycle associated genes. Also within the first 2 h, PMA induced immediate early genes including transcription factor genes encoding proteins implicated in macrophage differentiation (EGR2, JUN, MAFB) and down-regulated genes for transcription factors involved in immature myeloid cell proliferation (MYB, IRF8, GFI1). The dense time course revealed that the response to PMA was not linear and progressive. Rather, network-based clustering of the time course data highlighted a sequential cascade of transient up- and down-regulated expression of genes encoding feedback regulators, as well as transcription factors associated with macrophage differentiation and their inferred target genes. CAGE also identified known and candidate novel enhancers expressed in THP-1 cells and many novel inducible genes that currently lack functional annotation and/or had no previously known function in macrophages. The time course is available on the ZENBU platform allowing comparison to FANTOM4 and FANTOM5 data.
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Affiliation(s)
- Iveta Gažová
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J Bush
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Sara Clohisey
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Yokohama, Japan
| | - Lucas van Duin
- Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Robin Andersson
- Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - David A Hume
- Mater Research Institute - University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Kim M Summers
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom.,Mater Research Institute - University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
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41
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Patir A, Fraser AM, Barnett MW, McTeir L, Rainger J, Davey MG, Freeman TC. The transcriptional signature associated with human motile cilia. Sci Rep 2020; 10:10814. [PMID: 32616903 PMCID: PMC7331728 DOI: 10.1038/s41598-020-66453-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
Cilia are complex microtubule-based organelles essential to a range of processes associated with embryogenesis and tissue homeostasis. Mutations in components of these organelles or those involved in their assembly may result in a diverse set of diseases collectively known as ciliopathies. Accordingly, many cilia-associated proteins have been described, while those distinguishing cilia subtypes are poorly defined. Here we set out to define genes associated with motile cilia in humans based on their transcriptional signature. To define the signature, we performed network deconvolution of transcriptomics data derived from tissues possessing motile ciliated cell populations. For each tissue, genes coexpressed with the motile cilia-associated transcriptional factor, FOXJ1, were identified. The consensus across tissues provided a transcriptional signature of 248 genes. To validate these, we examined the literature, databases (CilDB, CentrosomeDB, CiliaCarta and SysCilia), single cell RNA-Seq data, and the localisation of mRNA and proteins in motile ciliated cells. In the case of six poorly characterised signature genes, we performed new localisation experiments on ARMC3, EFCAB6, FAM183A, MYCBPAP, RIBC2 and VWA3A. In summary, we report a set of motile cilia-associated genes that helps shape our understanding of these complex cellular organelles.
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Affiliation(s)
- Anirudh Patir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Amy M Fraser
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Mark W Barnett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Lynn McTeir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Joe Rainger
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Megan G Davey
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK
| | - Tom C Freeman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK.
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42
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Miller ET, You S, Cadaneanu RM, Kim M, Yoon J, Liu ST, Li X, Kwan L, Hodge J, Quist MJ, Grasso CS, Lewis MS, Knudsen BS, Freeman MR, Garraway IP. Chromosomal instability in untreated primary prostate cancer as an indicator of metastatic potential. BMC Cancer 2020; 20:398. [PMID: 32380981 PMCID: PMC7204307 DOI: 10.1186/s12885-020-06817-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022] Open
Abstract
Background Metastatic prostate cancer (PC) is highly lethal. The ability to identify primary tumors capable of dissemination is an unmet need in the quest to understand lethal biology and improve patient outcomes. Previous studies have linked chromosomal instability (CIN), which generates aneuploidy following chromosomal missegregation during mitosis, to PC progression. Evidence of CIN includes broad copy number alterations (CNAs) spanning > 300 base pairs of DNA, which may also be measured via RNA expression signatures associated with CNA frequency. Signatures of CIN in metastatic PC, however, have not been interrogated or well defined. We examined a published 70-gene CIN signature (CIN70) in untreated and castration-resistant prostate cancer (CRPC) cohorts from The Cancer Genome Atlas (TCGA) and previously published reports. We also performed transcriptome and CNA analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases to determine if CIN was linked to clinical stage and outcome. Methods PNBX were collected from 99 patients treated in the VA Greater Los Angeles (GLA-VA) Healthcare System between 2000 and 2016. Total RNA was extracted from high-grade cancer areas in PNBX cores, followed by RNA sequencing and/or copy number analysis using OncoScan. Multivariate logistic regression analyses permitted calculation of odds ratios for CIN status (high versus low) in an expanded GLA-VA PNBX cohort (n = 121). Results The CIN70 signature was significantly enriched in primary tumors and CRPC metastases from M1 PC cases. An intersection of gene signatures comprised of differentially expressed genes (DEGs) generated through comparison of M1 versus M0 PNBX and primary CRPC tumors versus metastases revealed a 157-gene “metastasis” signature that was further distilled to 7-genes (PC-CIN) regulating centrosomes, chromosomal segregation, and mitotic spindle assembly. High PC-CIN scores correlated with CRPC, PC-death and all-cause mortality in the expanded GLA-VA PNBX cohort. Interestingly, approximately 1/3 of M1 PNBX cases exhibited low CIN, illuminating differential pathways of lethal PC progression. Conclusions Measuring CIN in PNBX by transcriptome profiling is feasible, and the PC-CIN signature may identify patients with a high risk of lethal progression at the time of diagnosis.
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Affiliation(s)
- Eric T Miller
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Sungyong You
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Radu M Cadaneanu
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Minhyung Kim
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Junhee Yoon
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Sandy T Liu
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA.,Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Xinmin Li
- Department of Pathology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Lorna Kwan
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA
| | - Jennelle Hodge
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael J Quist
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Catherine S Grasso
- Department of Surgery, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael S Lewis
- Department of Pathology, Greater Los Angeles Veterans Affairs Health System, California, Los Angeles, USA
| | - Beatrice S Knudsen
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Michael R Freeman
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, California, Los Angeles, USA
| | - Isla P Garraway
- Department of Urology, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA. .,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA. .,Division of Urology, Greater Los Angeles Veterans Affairs Healthcare Center, Box 951738, 10833 Le Conte Ave 66-188 CHS UCLA, Los Angeles, CA, 90095, USA.
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43
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Chatonnet F, Pignarre A, Sérandour AA, Caron G, Avner S, Robert N, Kassambara A, Laurent A, Bizot M, Agirre X, Prosper F, Martin-Subero JI, Moreaux J, Fest T, Salbert G. The hydroxymethylome of multiple myeloma identifies FAM72D as a 1q21 marker linked to proliferation. Haematologica 2020; 105:774-783. [PMID: 31221779 PMCID: PMC7049362 DOI: 10.3324/haematol.2019.222133] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/19/2019] [Indexed: 01/16/2023] Open
Abstract
Cell identity relies on the cross-talk between genetics and epigenetics and their impact on gene expression. Oxidation of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) is the first step of an active DNA demethylation process occurring mainly at enhancers and gene bodies and, as such, participates in processes governing cell identity in normal and pathological conditions. Although genetic alterations are well documented in multiple myeloma (MM), epigenetic alterations associated with this disease have not yet been thoroughly analyzed. To gain insight into the biology of MM, genome-wide 5hmC profiles were obtained and showed that regions enriched in this modified base overlap with MM enhancers and super enhancers and are close to highly expressed genes. Through the definition of a MM-specific 5hmC signature, we identified FAM72D as a poor prognostic gene located on 1q21, a region amplified in high risk myeloma. We further uncovered that FAM72D functions as part of the FOXM1 transcription factor network controlling cell proliferation and survival and we evidenced an increased sensitivity of cells expressing high levels of FOXM1 and FAM72 to epigenetic drugs targeting histone deacetylases and DNA methyltransferases.
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Affiliation(s)
- Fabrice Chatonnet
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Amandine Pignarre
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Aurélien A Sérandour
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Nantes, France
- Institut de Cancérologie de l'Ouest, Site René-Gauducheau, Saint-Herblain, France
| | - Gersende Caron
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Stéphane Avner
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Nicolas Robert
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
| | | | - Audrey Laurent
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Maud Bizot
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
| | - Xabier Agirre
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Felipe Prosper
- Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | | | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- IGH, CNRS, Univ Montpellier, France
| | - Thierry Fest
- Université Rennes 1, Établissement Français du Sang de Bretaggne, Inserm, MICMAC -UMR_S 1236, Rennes, France
- Laboratoire d'Hématologie, Pôle de Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Gilles Salbert
- SPARTE, IGDR, CNRS UMR6290, University Rennes 1, Rennes, France
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44
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Monzón-Casanova E, Matheson LS, Tabbada K, Zarnack K, Smith CWJ, Turner M. Polypyrimidine tract-binding proteins are essential for B cell development. eLife 2020; 9:e53557. [PMID: 32081131 PMCID: PMC7058386 DOI: 10.7554/elife.53557] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a RNA-binding protein (RBP) expressed throughout B cell development. Deletion of Ptbp1 in mouse pro-B cells results in upregulation of PTBP2 and normal B cell development. We show that PTBP2 compensates for PTBP1 in B cell ontogeny as deletion of both Ptbp1 and Ptbp2 results in a complete block at the pro-B cell stage and a lack of mature B cells. In pro-B cells PTBP1 ensures precise synchronisation of the activity of cyclin dependent kinases at distinct stages of the cell cycle, suppresses S-phase entry and promotes progression into mitosis. PTBP1 controls mRNA abundance and alternative splicing of important cell cycle regulators including CYCLIN-D2, c-MYC, p107 and CDC25B. Our results reveal a previously unrecognised mechanism mediated by a RBP that is essential for B cell ontogeny and integrates transcriptional and post-translational determinants of progression through the cell cycle.
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Affiliation(s)
- Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Louise S Matheson
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
| | - Kristina Tabbada
- Next Generation Sequencing Facility, The Babraham InstituteCambridgeUnited Kingdom
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | | | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
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45
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Summers KM, Bush SJ, Wu C, Su AI, Muriuki C, Clark EL, Finlayson HA, Eory L, Waddell LA, Talbot R, Archibald AL, Hume DA. Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas. Front Genet 2020; 10:1355. [PMID: 32117413 PMCID: PMC7034361 DOI: 10.3389/fgene.2019.01355] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/11/2019] [Indexed: 12/15/2022] Open
Abstract
The domestic pig (Sus scrofa) is both an economically important livestock species and a model for biomedical research. Two highly contiguous pig reference genomes have recently been released. To support functional annotation of the pig genomes and comparative analysis with large human transcriptomic data sets, we aimed to create a pig gene expression atlas. To achieve this objective, we extended a previous approach developed for the chicken. We downloaded RNAseq data sets from public repositories, down-sampled to a common depth, and quantified expression against a reference transcriptome using the mRNA quantitation tool, Kallisto. We then used the network analysis tool Graphia to identify clusters of transcripts that were coexpressed across the merged data set. Consistent with the principle of guilt-by-association, we identified coexpression clusters that were highly tissue or cell-type restricted and contained transcription factors that have previously been implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes, such as the cell cycle and oxidative phosphorylation. The same approach was used to identify coexpression clusters within RNAseq data from multiple individual liver and brain samples, highlighting cell type, process, and region-specific gene expression. Evidence of conserved expression can add confidence to assignment of orthology between pig and human genes. Many transcripts currently identified as novel genes with ENSSSCG or LOC IDs were found to be coexpressed with annotated neighbouring transcripts in the same orientation, indicating they may be products of the same transcriptional unit. The meta-analytic approach to utilising public RNAseq data is extendable to include new data sets and new species and provides a framework to support the Functional Annotation of Animals Genomes (FAANG) initiative.
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Affiliation(s)
- Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Andrew I. Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Charity Muriuki
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Emily L. Clark
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | | | - Lel Eory
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Lindsey A. Waddell
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Richard Talbot
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Alan L. Archibald
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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46
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Niemira M, Collin F, Szalkowska A, Bielska A, Chwialkowska K, Reszec J, Niklinski J, Kwasniewski M, Kretowski A. Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA). Cancers (Basel) 2019; 12:E37. [PMID: 31877723 PMCID: PMC7017323 DOI: 10.3390/cancers12010037] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) represents a heterogeneous group of malignancies consisting essentially of adenocarcinoma (ADC) and squamous cell carcinoma (SCC). Although the diagnosis and treatment of ADC and SCC have been greatly improved in recent decades, there is still an urgent need to identify accurate transcriptome profile associated with the histological subtypes of NSCLC. The present study aims to identify the key dysregulated pathways and genes involved in the development of lung ADC and SCC and to relate them with the clinical traits. The transcriptional changes between tumour and normal lung tissues were investigated by RNA-seq. Gene ontology (GO), canonical pathways analysis with the prediction of upstream regulators, and weighted gene co-expression network analysis (WGCNA) to identify co-expressed modules and hub genes were used to explore the biological functions of the identified dysregulated genes. It was indicated that specific gene signatures differed significantly between ADC and SCC related to the distinct pathways. Of identified modules, four and two modules were the most related to clinical features in ADC and SCC, respectively. CTLA4, MZB1, NIP7, and BUB1B in ADC, as well as GNG11 and CCNB2 in SCC, are novel top hub genes in modules associated with tumour size, SUVmax, and recurrence-free survival. Our research provides a more effective understanding of the importance of biological pathways and the relationships between major genes in NSCLC in the perspective of searching for new molecular targets.
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Affiliation(s)
- Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Francois Collin
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Anna Szalkowska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Agnieszka Bielska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
| | - Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-276 Bialystok, Poland; (F.C.); (K.C.); (M.K.)
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.S.); (A.B.); (A.K.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
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47
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Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen SV, Enright AJ, Freeman TC. Visualization and analysis of RNA-Seq assembly graphs. Nucleic Acids Res 2019; 47:7262-7275. [PMID: 31305886 PMCID: PMC6698738 DOI: 10.1093/nar/gkz599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/31/2019] [Accepted: 07/10/2019] [Indexed: 01/20/2023] Open
Abstract
RNA-Seq is a powerful transcriptome profiling technology enabling transcript discovery and quantification. Whilst most commonly used for gene-level quantification, the data can be used for the analysis of transcript isoforms. However, when the underlying transcript assemblies are complex, current visualization approaches can be limiting, with splicing events a challenge to interpret. Here, we report on the development of a graph-based visualization method as a complementary approach to understanding transcript diversity from short-read RNA-Seq data. Following the mapping of reads to a reference genome, a read-to-read comparison is performed on all reads mapping to a given gene, producing a weighted similarity matrix between reads. This is used to produce an RNA assembly graph, where nodes represent reads and edges similarity scores between them. The resulting graphs are visualized in 3D space to better appreciate their sometimes large and complex topology, with other information being overlaid on to nodes, e.g. transcript models. Here we demonstrate the utility of this approach, including the unusual structure of these graphs and how they can be used to identify issues in assembly, repetitive sequences within transcripts and splice variants. We believe this approach has the potential to significantly improve our understanding of transcript complexity.
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Affiliation(s)
- Fahmi W Nazarie
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Barbara Shih
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tim Angus
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Mark W Barnett
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sz-Hau Chen
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Kim M Summers
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK.,Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba QLD 4102, Australia
| | - Karsten Klein
- Life Science Informatics Group, Department of Computer Science, Konstanz University, 78457 Konstanz, Germany
| | - Geoffrey J Faulkner
- Mater Research Institute - The University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba QLD 4102, Australia
| | - Harpreet K Saini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, UK
| | - Mick Watson
- Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Stijn van Dongen
- Cellular Genetics Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Anton J Enright
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Tom C Freeman
- Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
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