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Yin Y, Liu J, Xu C, Zeng D, Zhu Y, Wu X, Fan Q, Zhao S, Wang J, Liu Y, Li Y, Lu W. Whole-transcriptome RNA sequencing reveals CeRNA regulatory network under long-term space composite stress in Rats. LIFE SCIENCES IN SPACE RESEARCH 2024; 41:136-145. [PMID: 38670640 DOI: 10.1016/j.lssr.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/04/2024] [Accepted: 02/28/2024] [Indexed: 04/28/2024]
Abstract
To systematically evaluate the effect of simulated long-term spaceflight composite stress (LSCS) in hippocampus and gain more insights into the transcriptomic landscape and molecular mechanism, we performed whole-transcriptome sequencing based on the control group (Ctrl) and the simulated long-term spaceflight composite stress group (LSCS) from six hippocampus of rats. Subsequently, differential expression analysis was performed on the Ctrl and LSCS groups, followed by enrichment analysis and functional interaction prediction analysis to investigate gene-regulatory circuits in LSCS. In addition, competitive endogenous RNA (ceRNA) network was constructed to gain insights into genetic interaction. The result showed that 276 differentially expressed messenger RNAs (DEmRNAs), 139 differentially expressed long non-coding RNAs (DElncRNAs), 103 differentially expressed circular RNAs (DEcircRNAs), and 52 differentially expressed microRNAs (DEmiRNAs) were found in LSCS samples compared with the controls, which were then subjected to enrichment analysis of Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to find potential functions. PI3K-Akt signaling pathway and MAPK signaling pathway may play fundamental roles in the pathogenesis of LSCS. A ceRNA network was constructed with the predicted 340 DE pairs, which revealed the interaction roles of 220 DEmiRNA-DEmRNA pairs, 76 DEmiRNA-DElncRNA pairs, and 44 DEmiRNA-DEcircRNA pairs. Further, Thrombospondins2 was found to be a key target among those ceRNAs. Overall, we conducted for the first time a full transcriptomic analysis of the response of hippocampus to the LSCS that involved a potential ceRNA network, thus providing a basis to study the underlying mechanism of the LSCS.
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Affiliation(s)
- YiShu Yin
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, PR China; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin 150001, PR China
| | - JunLian Liu
- China Astronaut Research and Training Center, Beijing 100094, PR China; Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, PR China; Department of Psychology, University of Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chong Xu
- China Astronaut Research and Training Center, Beijing 100094, PR China
| | - DeYong Zeng
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, PR China; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin 150001, PR China
| | - YuanBing Zhu
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, PR China; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin 150001, PR China
| | - XiaoRui Wu
- China Astronaut Research and Training Center, Beijing 100094, PR China
| | - QuanChun Fan
- China Astronaut Research and Training Center, Beijing 100094, PR China
| | - Shuang Zhao
- China Astronaut Research and Training Center, Beijing 100094, PR China
| | - JiaPing Wang
- China Astronaut Research and Training Center, Beijing 100094, PR China
| | - Yu Liu
- China Astronaut Research and Training Center, Beijing 100094, PR China
| | - YongZhi Li
- China Astronaut Research and Training Center, Beijing 100094, PR China.
| | - Weihong Lu
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, PR China; National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin 150001, PR China.
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2
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Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Eagles NJ, Gonzalez-Padilla D, Maden SK, Kleinman JE, Hyde TM, Hicks SC, Maynard KR, Collado-Torres L. Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579665. [PMID: 38405805 PMCID: PMC10888823 DOI: 10.1101/2024.02.09.579665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background Cellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as human brain. Computational methods for deconvolution have been developed and benchmarked against simulated data, pseudobulked sc/snRNA-seq data, or immunohistochemistry reference data. A major limitation in developing improved deconvolution algorithms has been the lack of integrated datasets with orthogonal measurements of gene expression and estimates of cell type proportions on the same tissue sample. Deconvolution algorithm performance has not yet been evaluated across different RNA extraction methods (cytosolic, nuclear, or whole cell RNA), different library preparation types (mRNA enrichment vs. ribosomal RNA depletion), or with matched single cell reference datasets. Results A rich multi-assay dataset was generated in postmortem human dorsolateral prefrontal cortex (DLPFC) from 22 tissue blocks. Assays included spatially-resolved transcriptomics, snRNA-seq, bulk RNA-seq (across six library/extraction RNA-seq combinations), and RNAScope/Immunofluorescence (RNAScope/IF) for six broad cell types. The Mean Ratio method, implemented in the DeconvoBuddies R package, was developed for selecting cell type marker genes. Six computational deconvolution algorithms were evaluated in DLPFC and predicted cell type proportions were compared to orthogonal RNAScope/IF measurements. Conclusions Bisque and hspe were the most accurate methods, were robust to differences in RNA library types and extractions. This multi-assay dataset showed that cell size differences, marker genes differentially quantified across RNA libraries, and cell composition variability in reference snRNA-seq impact the accuracy of current deconvolution methods.
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Affiliation(s)
- Louise A. Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Kelsey D. Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Sophia Cinquemani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Nicholas J. Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | | | - Sean K. Maden
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kristen R. Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
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3
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Zeng C, Song X, Zhang Z, Cai Q, Cai J, Horbinski C, Hu B, Cheng SY, Zhang W. Dissection of transcriptomic and epigenetic heterogeneity of grade 4 gliomas: implications for prognosis. Acta Neuropathol Commun 2023; 11:133. [PMID: 37580817 PMCID: PMC10426201 DOI: 10.1186/s40478-023-01619-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/09/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Grade 4 glioma is the most aggressive and currently incurable brain tumor with a median survival of one year in adult patients. Elucidating novel transcriptomic and epigenetic contributors to the molecular heterogeneity underlying its aggressiveness may lead to improved clinical outcomes. METHODS To identify grade 4 glioma -associated 5-hydroxymethylcytosine (5hmC) and transcriptomic features as well as their cross-talks, genome-wide 5hmC and transcriptomic profiles of tissue samples from 61 patients with grade 4 gliomas and 9 normal controls were obtained for differential and co-regulation/co-modification analyses. Prognostic models on overall survival based on transcriptomic features and the 5hmC modifications summarized over genic regions (promoters, gene bodies) and brain-derived histone marks were developed using machine learning algorithms. RESULTS Despite global reduction, the majority of differential 5hmC features showed higher modification levels in grade 4 gliomas as compared to normal controls. In addition, the bi-directional correlations between 5hmC modifications over promoter regions or gene bodies and gene expression were greatly disturbed in grade 4 gliomas regardless of IDH1 mutation status. Phenotype-associated co-regulated 5hmC-5hmC modules and 5hmC-mRNA modules not only are enriched with different molecular pathways that are indicative of the pathogenesis of grade 4 gliomas, but also are of prognostic significance comparable to IDH1 mutation status. Lastly, the best-performing 5hmC model can predict patient survival at a much higher accuracy (c-index = 74%) when compared to conventional prognostic factor IDH1 (c-index = 57%), capturing the molecular characteristics of tumors that are independent of IDH1 mutation status and gene expression-based molecular subtypes. CONCLUSIONS The 5hmC-based prognostic model could offer a robust tool to predict survival in patients with grade 4 gliomas, potentially outperforming existing prognostic factors such as IDH1 mutations. The crosstalk between 5hmC and gene expression revealed another layer of complexity underlying the molecular heterogeneity in grade 4 gliomas, offering opportunities for identifying novel therapeutic targets.
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Affiliation(s)
- Chang Zeng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Xiao Song
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Qinyun Cai
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Jiajun Cai
- Huashan Hospital, Fudan University, 12 Wulumuqi Rd., Shanghai, 200040, China
| | - Craig Horbinski
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Bo Hu
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA
| | - Shi-Yuan Cheng
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
- The Robert H. Lurie Comprehensive Cancer Center and Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, 60611, USA.
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL, USA.
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4
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Hyams Y, Rubin-Blum M, Rosner A, Brodsky L, Rinkevich Y, Rinkevich B. Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii. Front Microbiol 2023; 14:1072053. [PMID: 37323901 PMCID: PMC10264598 DOI: 10.3389/fmicb.2023.1072053] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53-79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.
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Affiliation(s)
- Yosef Hyams
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, Israel
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Yuval Rinkevich
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
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Gustafsson C, Hauenstein J, Frengen N, Krstic A, Luc S, Månsson R. T-RHEX-RNAseq - a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells. BMC Genomics 2023; 24:205. [PMID: 37069502 PMCID: PMC10111750 DOI: 10.1186/s12864-023-09279-4] [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: 10/25/2022] [Accepted: 03/28/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming - to allow analysis of a broader range of transcripts - remains challenging. RESULTS We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps. CONCLUSION T-RHEX-RNAseq provides an easy-to-use, time efficient and automation compatible method for generating stranded RNAseq libraries from rare cells.
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Affiliation(s)
- Charlotte Gustafsson
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, ANA Futura, Alfred Nobels Allé 8 floor 7, Huddinge, SE-141 52, Sweden
| | - Julia Hauenstein
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, ANA Futura, Alfred Nobels Allé 8 floor 7, Huddinge, SE-141 52, Sweden
| | - Nicolai Frengen
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, ANA Futura, Alfred Nobels Allé 8 floor 7, Huddinge, SE-141 52, Sweden
| | - Aleksandra Krstic
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Sidinh Luc
- Center for Hematology and Regenerative Medicine (HERM), Karolinska Institutet, Stockholm, Sweden
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Månsson
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, ANA Futura, Alfred Nobels Allé 8 floor 7, Huddinge, SE-141 52, Sweden.
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden.
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Everaert C, Verwilt J, Verniers K, Vandamme N, Marcos Rubio A, Vandesompele J, Mestdagh P. Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation. Biol Proced Online 2023; 25:7. [PMID: 36890441 PMCID: PMC9996952 DOI: 10.1186/s12575-023-00193-3] [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: 01/05/2023] [Accepted: 02/14/2023] [Indexed: 03/10/2023] Open
Abstract
BACKGROUND RNA sequencing has become the gold standard for transcriptome analysis but has an inherent limitation of challenging quantification of low-abundant transcripts. In contrast to microarray technology, RNA sequencing reads are proportionally divided in function of transcript abundance. Therefore, low-abundant RNAs compete against highly abundant - and sometimes non-informative - RNA species. RESULTS We developed an easy-to-use strategy based on high-affinity RNA-binding oligonucleotides to block reverse transcription and PCR amplification of specific RNA transcripts, thereby substantially reducing their abundance in the final sequencing library. To demonstrate the broad application potential of our method, we applied it to different transcripts and library preparation strategies, including YRNAs in small RNA sequencing of human blood plasma, mitochondrial rRNAs in both 3' end sequencing and long-read sequencing, and MALAT1 in single-cell 3' end sequencing. We demonstrate that the blocking strategy is highly efficient, reproducible, specific, and generally results in better transcriptome coverage and complexity. CONCLUSION Our method does not require modifications of the library preparation procedure apart from simply adding blocking oligonucleotides to the RT reaction and can thus be easily integrated into virtually any RNA sequencing library preparation protocol.
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Affiliation(s)
- Celine Everaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jasper Verwilt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Niels Vandamme
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
- VIB Single Cell Core, Vlaams Instituut voor Biotechnologie, Ghent-Leuven, Belgium
| | - Alvaro Marcos Rubio
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.
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7
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David BM, Jensen PA. Improving an rRNA depletion protocol with statistical design of experiments. SLAS Technol 2022. [DOI: 10.1016/j.slast.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Barros-Silva D, Klavert J, Jenster G, Jerónimo C, Lafontaine DLJ, Martens-Uzunova ES. The role of OncoSnoRNAs and Ribosomal RNA 2'-O-methylation in Cancer. RNA Biol 2021; 18:61-74. [PMID: 34775914 PMCID: PMC8677010 DOI: 10.1080/15476286.2021.1991167] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ribosomes are essential nanomachines responsible for all protein production in cells. Ribosome biogenesis and function are energy costly processes, they are tightly regulated to match cellular needs. In cancer, major pathways that control ribosome biogenesis and function are often deregulated to ensure cell survival and to accommodate the continuous proliferation of tumour cells. Ribosomal RNAs (rRNAs) are abundantly modified with 2'-O-methylation (Nm, ribomethylation) being one of the most common modifications. In eukaryotic ribosomes, ribomethylation is performed by the methyltransferase Fibrillarin guided by box C/D small nucleolar RNAs (snoRNAs). Accumulating evidences indicate that snoRNA expression and ribosome methylation profiles are altered in cancer. Here we review our current knowledge on differential snoRNA expression and rRNA 2ʹ-O methylation in the context of human malignancies, and discuss the consequences and opportunities for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
- Daniela Barros-Silva
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.,Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Jonathan Klavert
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (Icbas-up), Porto, Portugal
| | - Denis L J Lafontaine
- Rna Molecular Biology, Fonds De La Recherche Scientifique (F.r.s./fnrs), Université Libre De Bruxelles (Ulb), BioPark Campus, Gosselies, Belgium
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
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Qiao Z, Yang D, Liu L, Liu Z, Wang J, He D, Wu H, Wang J, Ma Z. Genome-wide identification and characterization of long non-coding RNAs in MDCK cell lines with high and low tumorigenicities. Genomics 2020; 112:1077-1086. [DOI: 10.1016/j.ygeno.2019.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/03/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
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10
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Crump BC, Wojahn JM, Tomas F, Mueller RS. Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes. Front Microbiol 2018; 9:388. [PMID: 29599758 PMCID: PMC5863793 DOI: 10.3389/fmicb.2018.00388] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/20/2018] [Indexed: 11/13/2022] Open
Abstract
Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe-plant mutualisms support the health and growth of aquatic plants.
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Affiliation(s)
- Byron C. Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - John M. Wojahn
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Fiona Tomas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA), Universitat de les Illes Balears (UIB) – Consejo Superior de Investigaciones Científicas (CSIC), Esporles, Spain
| | - Ryan S. Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M, Gurgul A. A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits. Genet Mol Biol 2018; 41:125-136. [PMID: 29658965 PMCID: PMC5901489 DOI: 10.1590/1678-4685-gmb-2016-0101] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/11/2017] [Indexed: 12/31/2022] Open
Abstract
Pork is the most popular meat in the world. Unfortunately, the selection pressure
focused on high meat content led to a reduction in pork quality. The present
study used RNA-seq technology to identify metabolic process genes related to
pork quality traits and fat deposition. Differentially expressed genes (DEGs)
were identified between pigs of Pulawska and Polish Landrace breeds for two the
most important muscles (semimembranosus and longissimus
dorsi). A total of 71 significant DEGs were reported: 15 for
longissimus dorsi and 56 for
semimembranosus muscles. The genes overexpressed in
Pulawska pigs were involved in lipid metabolism (APOD,
LXRA, LIPE, AP2B1, ENSSSCG00000028753 and
OAS2) and proteolysis (CST6, CTSD, ISG15
and UCHL1). In Polish Landrace pigs, genes playing a role in
biological adhesion (KIT, VCAN, HES1, SFRP2, CDH11, SSX2IP and
PCDH17), actin cytoskeletal organisation (FRMD6,
LIMK1, KIF23 and CNN1) and calcium ion binding
(PVALB, CIB2, PCDH17, VCAN and CDH11) were
transcriptionally more active. The present study allows for better understanding
of the physiological processes associated with lipid metabolism and muscle fiber
organization. This information could be helpful in further research aiming to
estimate the genetic markers.
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Affiliation(s)
- Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Mirosław Tyra
- Department of Pig Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Artur Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
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12
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Cieślik M, Chinnaiyan AM. Cancer transcriptome profiling at the juncture of clinical translation. Nat Rev Genet 2017; 19:93-109. [PMID: 29279605 DOI: 10.1038/nrg.2017.96] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methodological breakthroughs over the past four decades have repeatedly revolutionized transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples. These transcriptomes provide a link between cellular phenotypes and their molecular underpinnings, such as mutations. In the context of cancer, this link represents an opportunity to dissect the complexity and heterogeneity of tumours and to discover new biomarkers or therapeutic strategies. Here, we review the rationale, methodology and translational impact of transcriptome profiling in cancer.
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Affiliation(s)
- Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan.,Department of Pathology, University of Michigan.,Comprehensive Cancer Center, University of Michigan.,Department of Urology, University of Michigan.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
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13
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Jaing C, Rowland RRR, Allen JE, Certoma A, Thissen JB, Bingham J, Rowe B, White JR, Wynne JW, Johnson D, Gaudreault NN, Williams DT. Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses. Sci Rep 2017; 7:10115. [PMID: 28860602 PMCID: PMC5579198 DOI: 10.1038/s41598-017-10186-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/04/2017] [Indexed: 11/09/2022] Open
Abstract
African swine fever virus (ASFV) is a macrophage-tropic virus responsible for ASF, a transboundary disease that threatens swine production world-wide. Since there are no vaccines available to control ASF after an outbreak, obtaining an understanding of the virus-host interaction is important for developing new intervention strategies. In this study, a whole transcriptomic RNA-Seq method was used to characterize differentially expressed genes in pigs infected with a low pathogenic ASFV isolate, OUR T88/3 (OURT), or the highly pathogenic Georgia 2007/1 (GRG). After infection, pigs infected with OURT showed no or few clinical signs; whereas, GRG produced clinical signs consistent with acute ASF. RNA-Seq detected the expression of ASFV genes from the whole blood of the GRG, but not the OURT pigs, consistent with the pathotypes of these strains and the replication of GRG in circulating monocytes. Even though GRG and OURT possess different pathogenic properties, there was significant overlap in the most upregulated host genes. A small number of differentially expressed microRNAs were also detected in GRG and OURT pigs. These data confirm previous studies describing the response of macrophages and lymphocytes to ASFV infection, as well as reveal unique gene pathways upregulated in response to infection with GRG.
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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America.
| | - Raymond R R Rowland
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Jonathan E Allen
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Andrea Certoma
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - James B Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - John Bingham
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Brenton Rowe
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - John R White
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - James W Wynne
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Dayna Johnson
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Natasha N Gaudreault
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - David T Williams
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia
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14
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Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis. PLoS One 2017; 12:e0178706. [PMID: 28570594 PMCID: PMC5453589 DOI: 10.1371/journal.pone.0178706] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/17/2017] [Indexed: 11/19/2022] Open
Abstract
Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification. These limitations and a number of other issues that span multiple steps from nucleic acid purification to library construction are addressed here. We optimized and automated a 96-well magnetic bead-based extraction protocol that can be scaled to large cohorts and is compatible with automation. Using sets of 32 and 91 individual FFPE samples respectively, we generated libraries from 100 ng of total RNA and DNA starting amounts with 95–100% success rate. The use of the resulting RNA in micro-RNA sequencing was also demonstrated. In addition to offering the potential of scalability and rapid throughput, the yield obtained with lower input requirements makes these methods applicable to clinical samples where tissue abundance is limiting.
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